Error in setQCEnvironment(cdfn)
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suparna mitra ▴ 290
@suparna-mitra-5328
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Hello group, I am new in bioconductor and trying use it for my Affymetrix microarray data. Genechip HuGene-1_0-st-v1. I have normalized my data using rma. Then when I trying to see the quality I found following error. Can anybody help me with this please. Thanks a lot in advance :) Best wishes, Suparna. > library(affy) > library(simpleaffy) Loading required package: genefilter Loading required package: gcrma Attaching package: 'simpleaffy' The following object(s) are masked _by_ '.GlobalEnv': getBioC > library("hugene10stv1cdf") > aqc<-qc(InVivodata) Error in setQCEnvironment(cdfn) : Could not find array definition file ' hugene10stv1cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. [[alternative HTML version deleted]]
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@james-w-macdonald-5106
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Hi Suparna, On 9/4/2012 11:35 AM, suparna mitra wrote: > Hello group, > I am new in bioconductor and trying use it for my Affymetrix microarray > data. > Genechip HuGene-1_0-st-v1. The simpleaffy package isn't really designed for this array. A significant portion of the QC measures are based on comparisons between the PM and MM probes, and the newer generation of arrays from Affy no longer have MM probes. Best, Jim > > I have normalized my data using rma. Then when I trying to see the quality > I found following error. Can anybody help me with this please. > Thanks a lot in advance :) > Best wishes, > Suparna. > >> library(affy) >> library(simpleaffy) > Loading required package: genefilter > Loading required package: gcrma > > Attaching package: 'simpleaffy' > > The following object(s) are masked _by_ '.GlobalEnv': > > getBioC > >> library("hugene10stv1cdf") >> aqc<-qc(InVivodata) > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' hugene10stv1cdf.qcdef '. > Simpleaffy does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC parameters > manually. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Dear Jim, Thanks a lot. Yes I also read something that HuGene array does not use the T7-Oligo(dT) primer. But sorry being new I just missed the point. Actually I was trying to follow a step by step tutorial for Affy data. But can you suggest the best way to perform qc for this chip? Thanks a lot, Suparna. On 4 September 2012 16:58, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Suparna, > > > On 9/4/2012 11:35 AM, suparna mitra wrote: > >> Hello group, >> I am new in bioconductor and trying use it for my Affymetrix microarray >> data. >> Genechip HuGene-1_0-st-v1. >> > > The simpleaffy package isn't really designed for this array. A significant > portion of the QC measures are based on comparisons between the PM and MM > probes, and the newer generation of arrays from Affy no longer have MM > probes. > > Best, > > Jim > > > >> I have normalized my data using rma. Then when I trying to see the quality >> I found following error. Can anybody help me with this please. >> Thanks a lot in advance :) >> Best wishes, >> Suparna. >> >> library(affy) >>> library(simpleaffy) >>> >> Loading required package: genefilter >> Loading required package: gcrma >> >> Attaching package: 'simpleaffy' >> >> The following object(s) are masked _by_ '.GlobalEnv': >> >> getBioC >> >> library("hugene10stv1cdf") >>> aqc<-qc(InVivodata) >>> >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' hugene10stv1cdf.qcdef '. >> Simpleaffy does not know the QC parameters for this array type. >> See the package vignette for details about how to specify QC parameters >> manually. >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Dr. Suparna Mitra Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Block A: Waterhouse Buildings, L69 3GL Liverpool Tel. +44 (0)151 795 5394, Internal ext: 55394 M: +44 (0) 7511387895 Email id: smitra@liverpool.ac.uk Alternative Email id: suparna.mitra.sm@gmail.com [[alternative HTML version deleted]]
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Hi Suparna, I use the oligo package to analyze these data, rather than the affy package. I also use my affycoretools package to help make certain QC plots that I like. I tend to do something like dat <- read.celfiles(list.celfiles(<wherever they="" are="">)) hist(dat) ## gives a density plot - they should all look similar You can look for problematic arrays using a probe level model. If you have multiple cores, you can first do Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) plm <- fitProbeLevelModel(dat) Then you can look at NUSE(plm) RLE(plm) It may also be interesting to look at residuals image(plm, type="residuals") Then eset <- rma(dat) If you use affycoretools you can do plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, <group types="">) and see if your replicates are grouping together. You can also do MA plots maplot(eset) which compare all your chips to a pseudo-array. If you have more than 25 arrays, you should do 25 at a time. Note that if you use the limma package to make comparisons you can weight arrays, so unless one or more are completely broken, you usually don't need to exclude. It's instructive to add the weights to a PCA plot. So if you have say 3 treated vs 3 control, you could do something like trt <- factor(rep(c("Treated","Control"), each = 3)) design <- model.matrix(~trt) wts <- arrayWeights(eset, design) plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) Best, Jim On 9/4/2012 12:06 PM, suparna mitra wrote: > Dear Jim, > Thanks a lot. Yes I also read something that HuGene array does not > use the T7-Oligo(dT) primer. But sorry being new I just missed the > point. Actually I was trying to follow a step by step tutorial for > Affy data. > > But can you suggest the best way to perform qc for this chip? > Thanks a lot, > Suparna. > > On 4 September 2012 16:58, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Suparna, > > > On 9/4/2012 11:35 AM, suparna mitra wrote: > > Hello group, > I am new in bioconductor and trying use it for my Affymetrix > microarray > data. > Genechip HuGene-1_0-st-v1. > > > The simpleaffy package isn't really designed for this array. A > significant portion of the QC measures are based on comparisons > between the PM and MM probes, and the newer generation of arrays > from Affy no longer have MM probes. > > Best, > > Jim > > > > I have normalized my data using rma. Then when I trying to see > the quality > I found following error. Can anybody help me with this please. > Thanks a lot in advance :) > Best wishes, > Suparna. > > library(affy) > library(simpleaffy) > > Loading required package: genefilter > Loading required package: gcrma > > Attaching package: 'simpleaffy' > > The following object(s) are masked _by_ '.GlobalEnv': > > getBioC > > library("hugene10stv1cdf") > aqc<-qc(InVivodata) > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' hugene10stv1cdf.qcdef '. > Simpleaffy does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC > parameters > manually. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394, Internal ext: 55394 > M: +44 (0) 7511387895 > Email id: smitra at liverpool.ac.uk <mailto:smitra at="" liverpool.ac.uk=""> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hello Jim, Thanks a lot for your reply and help. But now it seems I am having a new problem with read.celfiles. Until now ReadAffy worked perfectly, but not read.celfiles. It tells the proper files names but says "Error: These do not exist:" as shown below. Am I doing any silly mistake? Any help will be really great. Thanks a lot, Suparna. > mydata <- ReadAffy() > mydata AffyBatch object size of arrays=1050x1050 features (13 kb) cdf=HuGene-1_0-st-v1 (32321 affyids) number of samples=12 number of genes=32321 annotation=hugene10stv1 notes= > InVivodat<-read.celfiles(list.celfiles("/Users/smitra/Desktop/Micro_Ra wData/InVivoTargets")) Error: These do not exist: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL MC11_(HuGene-1_0-st-v1).CEL MC12_(HuGene-1_0-st-v1).CEL MC13_(HuGene-1_0-st-v1).CEL MC14_(HuGene-1_0-st-v1).CEL MC15_(HuGene-1_0-st-v1).CEL MC16_(HuGene-1_0-st-v1).CEL MC17_(HuGene-1_0-st-v1).CEL MC18_(HuGene-1_0-st-v1).CEL MC2_(HuGene-1_0-st-v1).CEL MC3_(HuGene-1_0-st-v1).CEL MC4_(HuGene-1_0-st-v1).CEL MC5_(HuGene-1_0-st-v1).CEL MC6_(HuGene-1_0-st-v1).CEL MC7_(HuGene-1_0-st-v1).CEL MC8_(HuGene-1_0-st-v1).CEL MC9_(HuGene-1_0-st-v1).CEL > On 4 September 2012 17:27, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Suparna, > > I use the oligo package to analyze these data, rather than the affy > package. I also use my affycoretools package to help make certain QC plots > that I like. > > I tend to do something like > > dat <- read.celfiles(list.celfiles(<**wherever they are>)) > hist(dat) ## gives a density plot - they should all look similar > > You can look for problematic arrays using a probe level model. If you have > multiple cores, you can first do > Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) > plm <- fitProbeLevelModel(dat) > > Then you can look at > NUSE(plm) > RLE(plm) > > It may also be interesting to look at residuals > image(plm, type="residuals") > > Then > eset <- rma(dat) > > If you use affycoretools you can do > > plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, <group> types>) > > and see if your replicates are grouping together. You can also do MA plots > > maplot(eset) > > which compare all your chips to a pseudo-array. If you have more than 25 > arrays, you should do 25 at a time. > > Note that if you use the limma package to make comparisons you can weight > arrays, so unless one or more are completely broken, you usually don't need > to exclude. It's instructive to add the weights to a PCA plot. So if you > have say 3 treated vs 3 control, you could do something like > > trt <- factor(rep(c("Treated","**Control"), each = 3)) > design <- model.matrix(~trt) > wts <- arrayWeights(eset, design) > > plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) > > Best, > > Jim > > > On 9/4/2012 12:06 PM, suparna mitra wrote: > >> Dear Jim, >> Thanks a lot. Yes I also read something that HuGene array does not use >> the T7-Oligo(dT) primer. But sorry being new I just missed the point. >> Actually I was trying to follow a step by step tutorial for Affy data. >> >> But can you suggest the best way to perform qc for this chip? >> Thanks a lot, >> Suparna. >> >> On 4 September 2012 16:58, James W. MacDonald <jmacdon@uw.edu <mailto:="">> jmacdon@uw.edu>> wrote: >> >> Hi Suparna, >> >> >> On 9/4/2012 11:35 AM, suparna mitra wrote: >> >> Hello group, >> I am new in bioconductor and trying use it for my Affymetrix >> microarray >> data. >> Genechip HuGene-1_0-st-v1. >> >> >> The simpleaffy package isn't really designed for this array. A >> significant portion of the QC measures are based on comparisons >> between the PM and MM probes, and the newer generation of arrays >> from Affy no longer have MM probes. >> >> Best, >> >> Jim >> >> >> >> I have normalized my data using rma. Then when I trying to see >> the quality >> I found following error. Can anybody help me with this please. >> Thanks a lot in advance :) >> Best wishes, >> Suparna. >> >> library(affy) >> library(simpleaffy) >> >> Loading required package: genefilter >> Loading required package: gcrma >> >> Attaching package: 'simpleaffy' >> >> The following object(s) are masked _by_ '.GlobalEnv': >> >> getBioC >> >> library("hugene10stv1cdf") >> aqc<-qc(InVivodata) >> >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' hugene10stv1cdf.qcdef '. >> Simpleaffy does not know the QC parameters for this array type. >> See the package vignette for details about how to specify QC >> parameters >> manually. >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394, Internal ext: 55394 >> M: +44 (0) 7511387895 >> Email id: smitra@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**> >> Alternative Email id: suparna.mitra.sm@gmail.com <mailto:>> suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Dr. Suparna Mitra Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Block A: Waterhouse Buildings, L69 3GL Liverpool Tel. +44 (0)151 795 5394, Internal ext: 55394 M: +44 (0) 7511387895 Email id: smitra@liverpool.ac.uk Alternative Email id: suparna.mitra.sm@gmail.com [[alternative HTML version deleted]]
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Hi Suparna, If the files aren't in your working directory, you need to add that information to your call to read.celfiles. read.celfiles(filenames = paste("/Users/smitra/Desktop/Micro_RawData/InVivoTargets/", list.celfiles("/Users/smitra/Desktop/Micro_RawData/InVivoTargets"), sep = "") Best, Jim On 9/4/2012 12:59 PM, suparna mitra wrote: > Hello Jim, > Thanks a lot for your reply and help. But now it seems I am having a > new problem with read.celfiles. > Until now ReadAffy worked perfectly, but not read.celfiles. It tells > the proper files names but says "Error: These do not exist:" as shown > below. Am I doing any silly mistake? > > Any help will be really great. > Thanks a lot, > Suparna. > > > mydata <- ReadAffy() > > > mydata > > AffyBatch object > > size of arrays=1050x1050 features (13 kb) > > cdf=HuGene-1_0-st-v1 (32321 affyids) > > number of samples=12 > > number of genes=32321 > > annotation=hugene10stv1 > > notes= > > > > > InVivodat<-read.celfiles(list.celfiles("/Users/smitra/Desktop/Micro_ RawData/InVivoTargets")) > > Error: These do not exist: > > MC1_(HuGene-1_0-st-v1).CEL > > MC10_(HuGene-1_0-st-v1).CEL > > MC11_(HuGene-1_0-st-v1).CEL > > MC12_(HuGene-1_0-st-v1).CEL > > MC13_(HuGene-1_0-st-v1).CEL > > MC14_(HuGene-1_0-st-v1).CEL > > MC15_(HuGene-1_0-st-v1).CEL > > MC16_(HuGene-1_0-st-v1).CEL > > MC17_(HuGene-1_0-st-v1).CEL > > MC18_(HuGene-1_0-st-v1).CEL > > MC2_(HuGene-1_0-st-v1).CEL > > MC3_(HuGene-1_0-st-v1).CEL > > MC4_(HuGene-1_0-st-v1).CEL > > MC5_(HuGene-1_0-st-v1).CEL > > MC6_(HuGene-1_0-st-v1).CEL > > MC7_(HuGene-1_0-st-v1).CEL > > MC8_(HuGene-1_0-st-v1).CEL > > MC9_(HuGene-1_0-st-v1).CEL > > > > > > On 4 September 2012 17:27, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Suparna, > > I use the oligo package to analyze these data, rather than the > affy package. I also use my affycoretools package to help make > certain QC plots that I like. > > I tend to do something like > > dat <- read.celfiles(list.celfiles(<wherever they="" are="">)) > hist(dat) ## gives a density plot - they should all look similar > > You can look for problematic arrays using a probe level model. If > you have multiple cores, you can first do > Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) > plm <- fitProbeLevelModel(dat) > > Then you can look at > NUSE(plm) > RLE(plm) > > It may also be interesting to look at residuals > image(plm, type="residuals") > > Then > eset <- rma(dat) > > If you use affycoretools you can do > > plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, > <group types="">) > > and see if your replicates are grouping together. You can also do > MA plots > > maplot(eset) > > which compare all your chips to a pseudo-array. If you have more > than 25 arrays, you should do 25 at a time. > > Note that if you use the limma package to make comparisons you can > weight arrays, so unless one or more are completely broken, you > usually don't need to exclude. It's instructive to add the weights > to a PCA plot. So if you have say 3 treated vs 3 control, you > could do something like > > trt <- factor(rep(c("Treated","Control"), each = 3)) > design <- model.matrix(~trt) > wts <- arrayWeights(eset, design) > > plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) > > Best, > > Jim > > > On 9/4/2012 12:06 PM, suparna mitra wrote: > > Dear Jim, > Thanks a lot. Yes I also read something that HuGene array > does not use the T7-Oligo(dT) primer. But sorry being new I > just missed the point. Actually I was trying to follow a step > by step tutorial for Affy data. > > But can you suggest the best way to perform qc for this chip? > Thanks a lot, > Suparna. > > On 4 September 2012 16:58, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > Hi Suparna, > > > On 9/4/2012 11:35 AM, suparna mitra wrote: > > Hello group, > I am new in bioconductor and trying use it for my > Affymetrix > microarray > data. > Genechip HuGene-1_0-st-v1. > > > The simpleaffy package isn't really designed for this array. A > significant portion of the QC measures are based on > comparisons > between the PM and MM probes, and the newer generation of > arrays > from Affy no longer have MM probes. > > Best, > > Jim > > > > I have normalized my data using rma. Then when I > trying to see > the quality > I found following error. Can anybody help me with this > please. > Thanks a lot in advance :) > Best wishes, > Suparna. > > library(affy) > library(simpleaffy) > > Loading required package: genefilter > Loading required package: gcrma > > Attaching package: 'simpleaffy' > > The following object(s) are masked _by_ '.GlobalEnv': > > getBioC > > library("hugene10stv1cdf") > aqc<-qc(InVivodata) > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' > hugene10stv1cdf.qcdef '. > Simpleaffy does not know the QC parameters for this > array type. > See the package vignette for details about how to > specify QC > parameters > manually. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org="">> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394 > <tel:%2b44%20%280%29151%20795%205394>, Internal ext: 55394 > M: +44 (0) 7511387895 <tel:%2b44%20%280%29%207511387895> > Email id: smitra at liverpool.ac.uk > <mailto:smitra at="" liverpool.ac.uk=""> <mailto:smitra at="" liverpool.ac.uk=""> <mailto:smitra at="" liverpool.ac.uk="">> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > <mailto:suparna.mitra.sm at="" gmail.com=""> <mailto:suparna.mitra.sm at="" gmail.com="">> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394, Internal ext: 55394 > M: +44 (0) 7511387895 > Email id: smitra at liverpool.ac.uk <mailto:smitra at="" liverpool.ac.uk=""> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Jim, Thanks a lot, but the files are there and also I just figured out somehow is working with "=". InVivodat=read.celfiles(list.celfiles("/Users/smitra/Desktop/Recent/Mi cro_RawData/InVivoTargets/")) No idea why. But now I get: Loading required package: pd.hugene.1.0.st.v1 Attempting to obtain 'pd.hugene.1.0.st.v1' from BioConductor website. Checking to see if your internet connection works... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .12 Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .12 trying URL ' http://bioconductor.org/packages/2.7/data/annotation/bin/macosx/leopar d/contrib/2.12/pd.hugene.1.0.st.v1_3.0.2.tgz ' Content type 'application/x-gzip' length 68064870 bytes (64.9 Mb) opened URL ================================================= downloaded 64.9 Mb The downloaded packages are in /var/folders/yq/fb09p6c556lf48k41ntj6v4w0000gp/T//RtmpPDzMft/downloade d_packages Loading required package: pd.hugene.1.0.st.v1 Platform design info loaded. Reading in : MC1_(HuGene-1_0-st-v1).CEL Reading in : MC10_(HuGene-1_0-st-v1).CEL Reading in : MC11_(HuGene-1_0-st-v1).CEL Reading in : MC12_(HuGene-1_0-st-v1).CEL Reading in : MC13_(HuGene-1_0-st-v1).CEL Reading in : MC14_(HuGene-1_0-st-v1).CEL Reading in : MC15_(HuGene-1_0-st-v1).CEL Reading in : MC16_(HuGene-1_0-st-v1).CEL Reading in : MC17_(HuGene-1_0-st-v1).CEL Reading in : MC18_(HuGene-1_0-st-v1).CEL Reading in : MC2_(HuGene-1_0-st-v1).CEL Reading in : MC3_(HuGene-1_0-st-v1).CEL Reading in : MC4_(HuGene-1_0-st-v1).CEL Reading in : MC5_(HuGene-1_0-st-v1).CEL Reading in : MC6_(HuGene-1_0-st-v1).CEL Reading in : MC7_(HuGene-1_0-st-v1).CEL Reading in : MC8_(HuGene-1_0-st-v1).CEL Reading in : MC9_(HuGene-1_0-st-v1).CEL Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'pd.hugene.1.0.st.v1' So now I am trying to find pd.hugene.1.0.st.v1 Thanks a lot, Suparna On 4 September 2012 18:10, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Suparna, > > If the files aren't in your working directory, you need to add that > information to your call to read.celfiles. > > read.celfiles(filenames = paste("/Users/smitra/Desktop/** > Micro_RawData/InVivoTargets/", > list.celfiles("/Users/smitra/** > Desktop/Micro_RawData/**InVivoTargets"), sep = "") > > > Best, > > Jim > > > > On 9/4/2012 12:59 PM, suparna mitra wrote: > >> Hello Jim, >> Thanks a lot for your reply and help. But now it seems I am having a new >> problem with read.celfiles. >> Until now ReadAffy worked perfectly, but not read.celfiles. It tells the >> proper files names but says "Error: These do not exist:" as shown below. Am >> I doing any silly mistake? >> >> Any help will be really great. >> Thanks a lot, >> Suparna. >> >> > mydata <- ReadAffy() >> >> > mydata >> >> AffyBatch object >> >> size of arrays=1050x1050 features (13 kb) >> >> cdf=HuGene-1_0-st-v1 (32321 affyids) >> >> number of samples=12 >> >> number of genes=32321 >> >> annotation=hugene10stv1 >> >> notes= >> >> >> > InVivodat<-read.celfiles(list.**celfiles("/Users/smitra/** >> Desktop/Micro_RawData/**InVivoTargets")) >> >> Error: These do not exist: >> >> MC1_(HuGene-1_0-st-v1).CEL >> >> MC10_(HuGene-1_0-st-v1).CEL >> >> MC11_(HuGene-1_0-st-v1).CEL >> >> MC12_(HuGene-1_0-st-v1).CEL >> >> MC13_(HuGene-1_0-st-v1).CEL >> >> MC14_(HuGene-1_0-st-v1).CEL >> >> MC15_(HuGene-1_0-st-v1).CEL >> >> MC16_(HuGene-1_0-st-v1).CEL >> >> MC17_(HuGene-1_0-st-v1).CEL >> >> MC18_(HuGene-1_0-st-v1).CEL >> >> MC2_(HuGene-1_0-st-v1).CEL >> >> MC3_(HuGene-1_0-st-v1).CEL >> >> MC4_(HuGene-1_0-st-v1).CEL >> >> MC5_(HuGene-1_0-st-v1).CEL >> >> MC6_(HuGene-1_0-st-v1).CEL >> >> MC7_(HuGene-1_0-st-v1).CEL >> >> MC8_(HuGene-1_0-st-v1).CEL >> >> MC9_(HuGene-1_0-st-v1).CEL >> >> > >> >> >> On 4 September 2012 17:27, James W. MacDonald <jmacdon@uw.edu <mailto:="">> jmacdon@uw.edu>> wrote: >> >> Hi Suparna, >> >> I use the oligo package to analyze these data, rather than the >> affy package. I also use my affycoretools package to help make >> certain QC plots that I like. >> >> I tend to do something like >> >> dat <- read.celfiles(list.celfiles(<**wherever they are>)) >> hist(dat) ## gives a density plot - they should all look similar >> >> You can look for problematic arrays using a probe level model. If >> you have multiple cores, you can first do >> Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) >> plm <- fitProbeLevelModel(dat) >> >> Then you can look at >> NUSE(plm) >> RLE(plm) >> >> It may also be interesting to look at residuals >> image(plm, type="residuals") >> >> Then >> eset <- rma(dat) >> >> If you use affycoretools you can do >> >> plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, >> <group types="">) >> >> and see if your replicates are grouping together. You can also do >> MA plots >> >> maplot(eset) >> >> which compare all your chips to a pseudo-array. If you have more >> than 25 arrays, you should do 25 at a time. >> >> Note that if you use the limma package to make comparisons you can >> weight arrays, so unless one or more are completely broken, you >> usually don't need to exclude. It's instructive to add the weights >> to a PCA plot. So if you have say 3 treated vs 3 control, you >> could do something like >> >> trt <- factor(rep(c("Treated","**Control"), each = 3)) >> design <- model.matrix(~trt) >> wts <- arrayWeights(eset, design) >> >> plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) >> >> Best, >> >> Jim >> >> >> On 9/4/2012 12:06 PM, suparna mitra wrote: >> >> Dear Jim, >> Thanks a lot. Yes I also read something that HuGene array >> does not use the T7-Oligo(dT) primer. But sorry being new I >> just missed the point. Actually I was trying to follow a step >> by step tutorial for Affy data. >> >> But can you suggest the best way to perform qc for this chip? >> Thanks a lot, >> Suparna. >> >> On 4 September 2012 16:58, James W. MacDonald <jmacdon@uw.edu>> <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu>> >> <mailto:jmacdon@uw.edu>>> wrote: >> >> Hi Suparna, >> >> >> On 9/4/2012 11:35 AM, suparna mitra wrote: >> >> Hello group, >> I am new in bioconductor and trying use it for my >> Affymetrix >> microarray >> data. >> Genechip HuGene-1_0-st-v1. >> >> >> The simpleaffy package isn't really designed for this array. A >> significant portion of the QC measures are based on >> comparisons >> between the PM and MM probes, and the newer generation of >> arrays >> from Affy no longer have MM probes. >> >> Best, >> >> Jim >> >> >> >> I have normalized my data using rma. Then when I >> trying to see >> the quality >> I found following error. Can anybody help me with this >> please. >> Thanks a lot in advance :) >> Best wishes, >> Suparna. >> >> library(affy) >> library(simpleaffy) >> >> Loading required package: genefilter >> Loading required package: gcrma >> >> Attaching package: 'simpleaffy' >> >> The following object(s) are masked _by_ '.GlobalEnv': >> >> getBioC >> >> library("hugene10stv1cdf") >> aqc<-qc(InVivodata) >> >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' >> hugene10stv1cdf.qcdef '. >> Simpleaffy does not know the QC parameters for this >> array type. >> See the package vignette for details about how to >> specify QC >> parameters >> manually. >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >> >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394 >> <tel:%2b44%20%280%29151%20795%**205394>, Internal ext: 55394 >> M: +44 (0) 7511387895 <tel:%2b44%20%280%29%**207511387895> >> Email id: smitra@liverpool.ac.uk >> <mailto:smitra@liverpool.ac.uk**> <mailto:smitra@liverpool.ac.uk>> >> <mailto:smitra@liverpool.ac.uk**>> >> Alternative Email id: suparna.mitra.sm@gmail.com >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> > >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394, Internal ext: 55394 >> M: +44 (0) 7511387895 >> Email id: smitra@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**> >> Alternative Email id: suparna.mitra.sm@gmail.com <mailto:>> suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Dr. Suparna Mitra Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Block A: Waterhouse Buildings, L69 3GL Liverpool Tel. +44 (0)151 795 5394, Internal ext: 55394 M: +44 (0) 7511387895 Email id: smitra@liverpool.ac.uk Alternative Email id: suparna.mitra.sm@gmail.com [[alternative HTML version deleted]]
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Hi Suparna, On 9/4/2012 1:14 PM, suparna mitra wrote: > Hi Jim, > Thanks a lot, but the files are there and also I just figured out > somehow is working with "=". > InVivodat=read.celfiles(list.celfiles("/Users/smitra/Desktop/Recent/ Micro_RawData/InVivoTargets/")) > No idea why. But now I get: > Loading required package: pd.hugene.1.0.st.v1 > Attempting to obtain 'pd.hugene.1.0.st.v1' from BioConductor website. > Checking to see if your internet connection works... > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.12 > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.12 > trying URL > 'http://bioconductor.org/packages/2.7/data/annotation/bin/macosx/leo pard/contrib/2.12/pd.hugene.1.0.st.v1_3.0.2.tgz' > Content type 'application/x-gzip' length 68064870 bytes (64.9 Mb) > opened URL > ================================================= > downloaded 64.9 Mb > > > The downloaded packages are in > /var/folders/yq/fb09p6c556lf48k41ntj6v4w0000gp/T//RtmpPDzMft/downloa ded_packages > Loading required package: pd.hugene.1.0.st.v1 > Platform design info loaded. > Reading in : MC1_(HuGene-1_0-st-v1).CEL > Reading in : MC10_(HuGene-1_0-st-v1).CEL > Reading in : MC11_(HuGene-1_0-st-v1).CEL > Reading in : MC12_(HuGene-1_0-st-v1).CEL > Reading in : MC13_(HuGene-1_0-st-v1).CEL > Reading in : MC14_(HuGene-1_0-st-v1).CEL > Reading in : MC15_(HuGene-1_0-st-v1).CEL > Reading in : MC16_(HuGene-1_0-st-v1).CEL > Reading in : MC17_(HuGene-1_0-st-v1).CEL > Reading in : MC18_(HuGene-1_0-st-v1).CEL > Reading in : MC2_(HuGene-1_0-st-v1).CEL > Reading in : MC3_(HuGene-1_0-st-v1).CEL > Reading in : MC4_(HuGene-1_0-st-v1).CEL > Reading in : MC5_(HuGene-1_0-st-v1).CEL > Reading in : MC6_(HuGene-1_0-st-v1).CEL > Reading in : MC7_(HuGene-1_0-st-v1).CEL > Reading in : MC8_(HuGene-1_0-st-v1).CEL > Reading in : MC9_(HuGene-1_0-st-v1).CEL > Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called 'pd.hugene.1.0.st.v1' > > So now I am trying to find pd.hugene.1.0.st.v1 It's there. That warning gets propagated incorrectly. You can see by doing search() at your R prompt. Best, Jim > > Thanks a lot, > Suparna > > On 4 September 2012 18:10, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Suparna, > > If the files aren't in your working directory, you need to add > that information to your call to read.celfiles. > > read.celfiles(filenames = > paste("/Users/smitra/Desktop/Micro_RawData/InVivoTargets/", > > list.celfiles("/Users/smitra/Desktop/Micro_RawData/InVivoTargets"), sep > = "") > > > Best, > > Jim > > > > On 9/4/2012 12:59 PM, suparna mitra wrote: > > Hello Jim, > Thanks a lot for your reply and help. But now it seems I am > having a new problem with read.celfiles. > Until now ReadAffy worked perfectly, but not read.celfiles. It > tells the proper files names but says "Error: These do not > exist:" as shown below. Am I doing any silly mistake? > > Any help will be really great. > Thanks a lot, > Suparna. > > > mydata <- ReadAffy() > > > mydata > > AffyBatch object > > size of arrays=1050x1050 features (13 kb) > > cdf=HuGene-1_0-st-v1 (32321 affyids) > > number of samples=12 > > number of genes=32321 > > annotation=hugene10stv1 > > notes= > > > > > InVivodat<-read.celfiles(list.celfiles("/Users/smitra/Deskto p/Micro_RawData/InVivoTargets")) > > Error: These do not exist: > > MC1_(HuGene-1_0-st-v1).CEL > > MC10_(HuGene-1_0-st-v1).CEL > > MC11_(HuGene-1_0-st-v1).CEL > > MC12_(HuGene-1_0-st-v1).CEL > > MC13_(HuGene-1_0-st-v1).CEL > > MC14_(HuGene-1_0-st-v1).CEL > > MC15_(HuGene-1_0-st-v1).CEL > > MC16_(HuGene-1_0-st-v1).CEL > > MC17_(HuGene-1_0-st-v1).CEL > > MC18_(HuGene-1_0-st-v1).CEL > > MC2_(HuGene-1_0-st-v1).CEL > > MC3_(HuGene-1_0-st-v1).CEL > > MC4_(HuGene-1_0-st-v1).CEL > > MC5_(HuGene-1_0-st-v1).CEL > > MC6_(HuGene-1_0-st-v1).CEL > > MC7_(HuGene-1_0-st-v1).CEL > > MC8_(HuGene-1_0-st-v1).CEL > > MC9_(HuGene-1_0-st-v1).CEL > > > > > > On 4 September 2012 17:27, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > Hi Suparna, > > I use the oligo package to analyze these data, rather than the > affy package. I also use my affycoretools package to help make > certain QC plots that I like. > > I tend to do something like > > dat <- read.celfiles(list.celfiles(<wherever they="" are="">)) > hist(dat) ## gives a density plot - they should all look > similar > > You can look for problematic arrays using a probe level > model. If > you have multiple cores, you can first do > Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) > plm <- fitProbeLevelModel(dat) > > Then you can look at > NUSE(plm) > RLE(plm) > > It may also be interesting to look at residuals > image(plm, type="residuals") > > Then > eset <- rma(dat) > > If you use affycoretools you can do > > plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, > <group types="">) > > and see if your replicates are grouping together. You can > also do > MA plots > > maplot(eset) > > which compare all your chips to a pseudo-array. If you > have more > than 25 arrays, you should do 25 at a time. > > Note that if you use the limma package to make comparisons > you can > weight arrays, so unless one or more are completely > broken, you > usually don't need to exclude. It's instructive to add the > weights > to a PCA plot. So if you have say 3 treated vs 3 control, you > could do something like > > trt <- factor(rep(c("Treated","Control"), each = 3)) > design <- model.matrix(~trt) > wts <- arrayWeights(eset, design) > > plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) > > Best, > > Jim > > > On 9/4/2012 12:06 PM, suparna mitra wrote: > > Dear Jim, > Thanks a lot. Yes I also read something that HuGene > array > does not use the T7-Oligo(dT) primer. But sorry being > new I > just missed the point. Actually I was trying to follow > a step > by step tutorial for Affy data. > > But can you suggest the best way to perform qc for > this chip? > Thanks a lot, > Suparna. > > On 4 September 2012 16:58, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">> > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> > > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">>>> wrote: > > Hi Suparna, > > > On 9/4/2012 11:35 AM, suparna mitra wrote: > > Hello group, > I am new in bioconductor and trying use it > for my > Affymetrix > microarray > data. > Genechip HuGene-1_0-st-v1. > > > The simpleaffy package isn't really designed for > this array. A > significant portion of the QC measures are based on > comparisons > between the PM and MM probes, and the newer > generation of > arrays > from Affy no longer have MM probes. > > Best, > > Jim > > > > I have normalized my data using rma. Then when I > trying to see > the quality > I found following error. Can anybody help me > with this > please. > Thanks a lot in advance :) > Best wishes, > Suparna. > > library(affy) > library(simpleaffy) > > Loading required package: genefilter > Loading required package: gcrma > > Attaching package: 'simpleaffy' > > The following object(s) are masked _by_ > '.GlobalEnv': > > getBioC > > library("hugene10stv1cdf") > aqc<-qc(InVivodata) > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' > hugene10stv1cdf.qcdef '. > Simpleaffy does not know the QC parameters for > this > array type. > See the package vignette for details about how to > specify QC > parameters > manually. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org="">> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org=""> > > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org="">>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of > Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394 > <tel:%2b44%20%280%29151%20795%205394> > <tel:%2b44%20%280%29151%20795%205394>, Internal ext: 55394 > M: +44 (0) 7511387895 > <tel:%2b44%20%280%29%207511387895> > <tel:%2b44%20%280%29%207511387895> > Email id: smitra at liverpool.ac.uk > <mailto:smitra at="" liverpool.ac.uk=""> > <mailto:smitra at="" liverpool.ac.uk=""> <mailto:smitra at="" liverpool.ac.uk="">> > <mailto:smitra at="" liverpool.ac.uk="" <mailto:smitra="" at="" liverpool.ac.uk=""> > > <mailto:smitra at="" liverpool.ac.uk="" <mailto:smitra="" at="" liverpool.ac.uk="">>> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > <mailto:suparna.mitra.sm at="" gmail.com=""> <mailto:suparna.mitra.sm at="" gmail.com="">> > <mailto:suparna.mitra.sm at="" gmail.com=""> <mailto:suparna.mitra.sm at="" gmail.com=""> > > <mailto:suparna.mitra.sm at="" gmail.com=""> <mailto:suparna.mitra.sm at="" gmail.com="">>> > > > -- James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394 > <tel:%2b44%20%280%29151%20795%205394>, Internal ext: 55394 > M: +44 (0) 7511387895 <tel:%2b44%20%280%29%207511387895> > Email id: smitra at liverpool.ac.uk > <mailto:smitra at="" liverpool.ac.uk=""> <mailto:smitra at="" liverpool.ac.uk=""> <mailto:smitra at="" liverpool.ac.uk="">> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > <mailto:suparna.mitra.sm at="" gmail.com=""> <mailto:suparna.mitra.sm at="" gmail.com="">> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Dr. Suparna Mitra > Wolfson Centre for Personalised Medicine > Department of Molecular and Clinical Pharmacology > Institute of Translational Medicine University of Liverpool > Block A: Waterhouse Buildings, L69 3GL Liverpool > > Tel. +44 (0)151 795 5394, Internal ext: 55394 > M: +44 (0) 7511387895 > Email id: smitra at liverpool.ac.uk <mailto:smitra at="" liverpool.ac.uk=""> > Alternative Email id: suparna.mitra.sm at gmail.com > <mailto:suparna.mitra.sm at="" gmail.com=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Jim, Thanks. Now it seems good to go. I will try the rest now :) Best, S > library(pd.hugene.1.0.st.v1) > InVivodat=read.celfiles(list.celfiles("/Users/smitra/Desktop/Recent /Liverpool-work-related/Micro_RawData/InVivoTargets/")) Platform design info loaded. Reading in : MC1_(HuGene-1_0-st-v1).CEL Reading in : MC10_(HuGene-1_0-st-v1).CEL Reading in : MC11_(HuGene-1_0-st-v1).CEL Reading in : MC12_(HuGene-1_0-st-v1).CEL Reading in : MC13_(HuGene-1_0-st-v1).CEL Reading in : MC14_(HuGene-1_0-st-v1).CEL Reading in : MC15_(HuGene-1_0-st-v1).CEL Reading in : MC16_(HuGene-1_0-st-v1).CEL Reading in : MC17_(HuGene-1_0-st-v1).CEL Reading in : MC18_(HuGene-1_0-st-v1).CEL Reading in : MC2_(HuGene-1_0-st-v1).CEL Reading in : MC3_(HuGene-1_0-st-v1).CEL Reading in : MC4_(HuGene-1_0-st-v1).CEL Reading in : MC5_(HuGene-1_0-st-v1).CEL Reading in : MC6_(HuGene-1_0-st-v1).CEL Reading in : MC7_(HuGene-1_0-st-v1).CEL Reading in : MC8_(HuGene-1_0-st-v1).CEL Reading in : MC9_(HuGene-1_0-st-v1).CEL On 4 September 2012 18:19, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Suparna, > > > On 9/4/2012 1:14 PM, suparna mitra wrote: > >> Hi Jim, >> Thanks a lot, but the files are there and also I just figured out >> somehow is working with "=". >> InVivodat=read.celfiles(list.**celfiles("/Users/smitra/** >> Desktop/Recent/Micro_RawData/**InVivoTargets/")) >> No idea why. But now I get: >> Loading required package: pd.hugene.1.0.st.v1 >> Attempting to obtain 'pd.hugene.1.0.st.v1' from BioConductor website. >> Checking to see if your internet connection works... >> Warning: unable to access index for repository >> http://brainarray.mbni.med.**umich.edu/bioc/bin/macosx/** >> leopard/contrib/2.12<http: brainarray.mbni.med.umich.edu="" bioc="" bin="" macosx="" leopard="" contrib="" 2.12=""> >> Warning: unable to access index for repository >> http://brainarray.mbni.med.**umich.edu/bioc/bin/macosx/** >> leopard/contrib/2.12<http: brainarray.mbni.med.umich.edu="" bioc="" bin="" macosx="" leopard="" contrib="" 2.12=""> >> trying URL 'http://bioconductor.org/**packages/2.7/data/annotation/** >> bin/macosx/leopard/contrib/2.**12/pd.hugene.1.0.st.v1_3.0.2.**tgz<h ttp:="" bioconductor.org="" packages="" 2.7="" data="" annotation="" bin="" macosx="" leopard="" contrib="" 2.12="" pd.hugene.1.0.st.v1_3.0.2.tgz=""> >> ' >> Content type 'application/x-gzip' length 68064870 bytes (64.9 Mb) >> opened URL >> ==============================**=================== >> downloaded 64.9 Mb >> >> >> The downloaded packages are in >> /var/folders/yq/**fb09p6c556lf48k41ntj6v4w0000gp** >> /T//RtmpPDzMft/downloaded_**packages >> Loading required package: pd.hugene.1.0.st.v1 >> Platform design info loaded. >> Reading in : MC1_(HuGene-1_0-st-v1).CEL >> Reading in : MC10_(HuGene-1_0-st-v1).CEL >> Reading in : MC11_(HuGene-1_0-st-v1).CEL >> Reading in : MC12_(HuGene-1_0-st-v1).CEL >> Reading in : MC13_(HuGene-1_0-st-v1).CEL >> Reading in : MC14_(HuGene-1_0-st-v1).CEL >> Reading in : MC15_(HuGene-1_0-st-v1).CEL >> Reading in : MC16_(HuGene-1_0-st-v1).CEL >> Reading in : MC17_(HuGene-1_0-st-v1).CEL >> Reading in : MC18_(HuGene-1_0-st-v1).CEL >> Reading in : MC2_(HuGene-1_0-st-v1).CEL >> Reading in : MC3_(HuGene-1_0-st-v1).CEL >> Reading in : MC4_(HuGene-1_0-st-v1).CEL >> Reading in : MC5_(HuGene-1_0-st-v1).CEL >> Reading in : MC6_(HuGene-1_0-st-v1).CEL >> Reading in : MC7_(HuGene-1_0-st-v1).CEL >> Reading in : MC8_(HuGene-1_0-st-v1).CEL >> Reading in : MC9_(HuGene-1_0-st-v1).CEL >> Warning message: >> In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, : >> there is no package called 'pd.hugene.1.0.st.v1' >> >> So now I am trying to find pd.hugene.1.0.st.v1 >> > > It's there. That warning gets propagated incorrectly. You can see by doing > > search() > > at your R prompt. > > Best, > > Jim > > > >> Thanks a lot, >> Suparna >> >> >> On 4 September 2012 18:10, James W. MacDonald <jmacdon@uw.edu <mailto:="">> jmacdon@uw.edu>> wrote: >> >> Hi Suparna, >> >> If the files aren't in your working directory, you need to add >> that information to your call to read.celfiles. >> >> read.celfiles(filenames = >> paste("/Users/smitra/Desktop/**Micro_RawData/InVivoTargets/", >> list.celfiles("/Users/smitra/** >> Desktop/Micro_RawData/**InVivoTargets"), sep >> = "") >> >> >> Best, >> >> Jim >> >> >> >> On 9/4/2012 12:59 PM, suparna mitra wrote: >> >> Hello Jim, >> Thanks a lot for your reply and help. But now it seems I am >> having a new problem with read.celfiles. >> Until now ReadAffy worked perfectly, but not read.celfiles. It >> tells the proper files names but says "Error: These do not >> exist:" as shown below. Am I doing any silly mistake? >> >> Any help will be really great. >> Thanks a lot, >> Suparna. >> >> > mydata <- ReadAffy() >> >> > mydata >> >> AffyBatch object >> >> size of arrays=1050x1050 features (13 kb) >> >> cdf=HuGene-1_0-st-v1 (32321 affyids) >> >> number of samples=12 >> >> number of genes=32321 >> >> annotation=hugene10stv1 >> >> notes= >> >> >> > >> InVivodat<-read.celfiles(list.**celfiles("/Users/smitra/** >> Desktop/Micro_RawData/**InVivoTargets")) >> >> Error: These do not exist: >> >> MC1_(HuGene-1_0-st-v1).CEL >> >> MC10_(HuGene-1_0-st-v1).CEL >> >> MC11_(HuGene-1_0-st-v1).CEL >> >> MC12_(HuGene-1_0-st-v1).CEL >> >> MC13_(HuGene-1_0-st-v1).CEL >> >> MC14_(HuGene-1_0-st-v1).CEL >> >> MC15_(HuGene-1_0-st-v1).CEL >> >> MC16_(HuGene-1_0-st-v1).CEL >> >> MC17_(HuGene-1_0-st-v1).CEL >> >> MC18_(HuGene-1_0-st-v1).CEL >> >> MC2_(HuGene-1_0-st-v1).CEL >> >> MC3_(HuGene-1_0-st-v1).CEL >> >> MC4_(HuGene-1_0-st-v1).CEL >> >> MC5_(HuGene-1_0-st-v1).CEL >> >> MC6_(HuGene-1_0-st-v1).CEL >> >> MC7_(HuGene-1_0-st-v1).CEL >> >> MC8_(HuGene-1_0-st-v1).CEL >> >> MC9_(HuGene-1_0-st-v1).CEL >> >> > >> >> >> On 4 September 2012 17:27, James W. MacDonald <jmacdon@uw.edu>> <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu>> <mailto:jmacdon@uw.edu>>> wrote: >> >> Hi Suparna, >> >> I use the oligo package to analyze these data, rather than the >> affy package. I also use my affycoretools package to help make >> certain QC plots that I like. >> >> I tend to do something like >> >> dat <- read.celfiles(list.celfiles(<**wherever they are>)) >> hist(dat) ## gives a density plot - they should all look >> similar >> >> You can look for problematic arrays using a probe level >> model. If >> you have multiple cores, you can first do >> Sys.setenv(R_THREADS = <number of="" cores="" you="" want="" to="" use="">) >> plm <- fitProbeLevelModel(dat) >> >> Then you can look at >> NUSE(plm) >> RLE(plm) >> >> It may also be interesting to look at residuals >> image(plm, type="residuals") >> >> Then >> eset <- rma(dat) >> >> If you use affycoretools you can do >> >> plotPCA(eset, <vector of="" numbers="" indicating="" group="" membership="">, >> <group types="">) >> >> and see if your replicates are grouping together. You can >> also do >> MA plots >> >> maplot(eset) >> >> which compare all your chips to a pseudo-array. If you >> have more >> than 25 arrays, you should do 25 at a time. >> >> Note that if you use the limma package to make comparisons >> you can >> weight arrays, so unless one or more are completely >> broken, you >> usually don't need to exclude. It's instructive to add the >> weights >> to a PCA plot. So if you have say 3 treated vs 3 control, you >> could do something like >> >> trt <- factor(rep(c("Treated","**Control"), each = 3)) >> design <- model.matrix(~trt) >> wts <- arrayWeights(eset, design) >> >> plotPCA(eset, groups, groupnames, addtext = round(wts, 2)) >> >> Best, >> >> Jim >> >> >> On 9/4/2012 12:06 PM, suparna mitra wrote: >> >> Dear Jim, >> Thanks a lot. Yes I also read something that HuGene >> array >> does not use the T7-Oligo(dT) primer. But sorry being >> new I >> just missed the point. Actually I was trying to follow >> a step >> by step tutorial for Affy data. >> >> But can you suggest the best way to perform qc for >> this chip? >> Thanks a lot, >> Suparna. >> >> On 4 September 2012 16:58, James W. MacDonald >> <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> >> <mailto:jmacdon@uw.edu <mailto:jmacdon@uw.edu="">> >> <mailto:jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> >> >> <mailto:jmacdon@uw.edu <mailto:jmacdon@uw.edu="">>>> wrote: >> >> Hi Suparna, >> >> >> On 9/4/2012 11:35 AM, suparna mitra wrote: >> >> Hello group, >> I am new in bioconductor and trying use it >> for my >> Affymetrix >> microarray >> data. >> Genechip HuGene-1_0-st-v1. >> >> >> The simpleaffy package isn't really designed for >> this array. A >> significant portion of the QC measures are based on >> comparisons >> between the PM and MM probes, and the newer >> generation of >> arrays >> from Affy no longer have MM probes. >> >> Best, >> >> Jim >> >> >> >> I have normalized my data using rma. Then when I >> trying to see >> the quality >> I found following error. Can anybody help me >> with this >> please. >> Thanks a lot in advance :) >> Best wishes, >> Suparna. >> >> library(affy) >> library(simpleaffy) >> >> Loading required package: genefilter >> Loading required package: gcrma >> >> Attaching package: 'simpleaffy' >> >> The following object(s) are masked _by_ >> '.GlobalEnv': >> >> getBioC >> >> library("hugene10stv1cdf") >> aqc<-qc(InVivodata) >> >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' >> hugene10stv1cdf.qcdef '. >> Simpleaffy does not know the QC parameters for >> this >> array type. >> See the package vignette for details about how to >> specify QC >> parameters >> manually. >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> > >> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >>> >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of >> Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394 >> <tel:%2b44%20%280%29151%20795%**205394> >> <tel:%2b44%20%280%29151%20795%**205394>, Internal ext: 55394 >> M: +44 (0) 7511387895 >> <tel:%2b44%20%280%29%**207511387895> >> <tel:%2b44%20%280%29%**207511387895> >> Email id: smitra@liverpool.ac.uk >> <mailto:smitra@liverpool.ac.uk**> >> <mailto:smitra@liverpool.ac.uk>> <mailto:smitra@liverpool.ac.uk**>> >> <mailto:smitra@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**=""> >> >> <mailto:smitra@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**="">> >>> >> >> Alternative Email id: suparna.mitra.sm@gmail.com >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> > >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> >> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> > >> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> >>> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394 >> <tel:%2b44%20%280%29151%20795%**205394>, Internal ext: 55394 >> M: +44 (0) 7511387895 <tel:%2b44%20%280%29%**207511387895> >> Email id: smitra@liverpool.ac.uk >> <mailto:smitra@liverpool.ac.uk**> <mailto:smitra@liverpool.ac.uk>> <mailto:smitra@liverpool.ac.uk**>> >> Alternative Email id: suparna.mitra.sm@gmail.com >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> > >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com=""> >> >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Dr. Suparna Mitra >> Wolfson Centre for Personalised Medicine >> Department of Molecular and Clinical Pharmacology >> Institute of Translational Medicine University of Liverpool >> Block A: Waterhouse Buildings, L69 3GL Liverpool >> >> Tel. +44 (0)151 795 5394, Internal ext: 55394 >> M: +44 (0) 7511387895 >> Email id: smitra@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**> >> Alternative Email id: suparna.mitra.sm@gmail.com <mailto:>> suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Dr. Suparna Mitra Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Block A: Waterhouse Buildings, L69 3GL Liverpool Tel. +44 (0)151 795 5394, Internal ext: 55394 M: +44 (0) 7511387895 Email id: smitra@liverpool.ac.uk Alternative Email id: suparna.mitra.sm@gmail.com [[alternative HTML version deleted]]
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