Agi4x44PreProcess
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Francois Pepin ★ 1.3k
@francois-pepin-1012
Last seen 10.3 years ago
(Apologies, I had originally put BioC in bcc instead of cc, whoever is moderating the list should feel free to delete the original) Dear Hemang, Please use the bioconductor mailing list. This will allow other people to help you in addition to ensuring that this e-mail will be archived and searchable for other people who might have the same issue. While I have commented on the usage of Agi4x44PreProcess and tried to help people using it, I have never actually used it. In this particular case, I would recommend that you read the help for the function that you just used: ?read.AgilentFE. I am 99% sure that your files were not "generated by the Agilent Feature Extraction image analysis software", explaining why the function was unable to read your files and giving you this error. These files most likely originate from GEO. The GEOquery package will be a lot more useful in your case. You would then probably need to convert it into an RGList or a similar object for the Agi4x44PreProcess package will be able to work. I hope this helps, Francois On 12/02/2009 12:14 PM, Hemang Parikh wrote: > > > Hi Francois, > > I found your e-mail address from Bioconductor mailing list. I am using > Agi4x44PreProcess package. However, I am getting an error message while > reading Agilent files with read.AgilentFE. I am just wondering if you > can help me to resolve the issue. > > Thanks for your help, > > Hemang > > dd=read.AgilentFE(targets, makePLOT=FALSE) > > Read GSM187289.txt > > Read GSM187290.txt > > Read GSM187291.txt > > Read GSM187292.txt > > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > > SCANN THE DATA USING AFE 9.5.3.1 > > Error in read.AgilentFE(targets, makePLOT = FALSE) : > > the script will stop now >
convert GEOquery Agi4x44PreProcess convert GEOquery Agi4x44PreProcess • 1.5k views
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Francois Pepin ★ 1.3k
@francois-pepin-1012
Last seen 10.3 years ago
Dear Hemang, Please use the bioconductor mailing list. This will allow other people to help you in addition to ensuring that this e-mail will be archived and searchable for other people who might have the same issue. While I have commented on the usage of Agi4x44PreProcess and tried to help people using it, I have never actually used it. In this particular case, I would recommend that you read the help for the function that you just used: ?read.AgilentFE. I am 99% sure that your files were not "generated by the Agilent Feature Extraction image analysis software", explaining why the function was unable to read your files and giving you this error. These files most likely originate from GEO. The GEOquery package will be a lot more useful in your case. You would then probably need to convert it into an RGList or a similar object for the Agi4x44PreProcess package will be able to work. I hope this helps, Francois On 12/02/2009 12:14 PM, Hemang Parikh wrote: > > > Hi Francois, > > I found your e-mail address from Bioconductor mailing list. I am using > Agi4x44PreProcess package. However, I am getting an error message while > reading Agilent files with read.AgilentFE. I am just wondering if you > can help me to resolve the issue. > > Thanks for your help, > > Hemang > > dd=read.AgilentFE(targets, makePLOT=FALSE) > > Read GSM187289.txt > > Read GSM187290.txt > > Read GSM187291.txt > > Read GSM187292.txt > > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > > SCANN THE DATA USING AFE 9.5.3.1 > > Error in read.AgilentFE(targets, makePLOT = FALSE) : > > the script will stop now >
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Yong Li ▴ 190
@yong-li-3321
Last seen 10.3 years ago
Dear Hemang, from the txt file names you were trying to read it seems they are from GEO. When searching in GEO I found that they are from GSE7702. The description as well as the txt files tell that they are two channel Agilent data. Agi4x44PreProcess package only works with one channel Agilent data. For two channel data limma package is recommended. Hope this helps. Yong Francois Pepin wrote: > (Apologies, I had originally put BioC in bcc instead of cc, whoever is > moderating the list should feel free to delete the original) > > Dear Hemang, > > Please use the bioconductor mailing list. This will allow other people > to help you in addition to ensuring that this e-mail will be archived > and searchable for other people who might have the same issue. > > While I have commented on the usage of Agi4x44PreProcess and tried to > help people using it, I have never actually used it. > > In this particular case, I would recommend that you read the help for > the function that you just used: ?read.AgilentFE. > > I am 99% sure that your files were not "generated by the Agilent Feature > Extraction image analysis software", explaining why the function was > unable to read your files and giving you this error. > > These files most likely originate from GEO. The GEOquery package will be > a lot more useful in your case. > > You would then probably need to convert it into an RGList or a similar > object for the Agi4x44PreProcess package will be able to work. > > I hope this helps, > > Francois > > On 12/02/2009 12:14 PM, Hemang Parikh wrote: >> >> >> Hi Francois, >> >> I found your e-mail address from Bioconductor mailing list. I am using >> Agi4x44PreProcess package. However, I am getting an error message while >> reading Agilent files with read.AgilentFE. I am just wondering if you >> can help me to resolve the issue. >> >> Thanks for your help, >> >> Hemang >> >> dd=read.AgilentFE(targets, makePLOT=FALSE) >> >> Read GSM187289.txt >> >> Read GSM187290.txt >> >> Read GSM187291.txt >> >> Read GSM187292.txt >> >> INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord >> >> SCANN THE DATA USING AFE 9.5.3.1 >> >> Error in read.AgilentFE(targets, makePLOT = FALSE) : >> >> the script will stop now >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 8.0 years ago
United States
Hello, Can anyone help me in troubleshooting the function for filtering probes. Below is the session info and I am just trying the functions in the user guide. Thank you, Neel Session info. > setwd("/Users/Neel/agilent") > library("Agi4x44PreProcess") > targets=read.targets(infile="infile.txt") Target File X FileName Treatment GErep conta cont1 conta.txt control 1 contb cont2 contb.txt control 2 contc cont3 contc.txt control 3 contd cont4 contd.txt control 4 pcba pcb1 pcba.txt pcb 1 pcbb pcb2 pcbb.txt pcb 2 pcbc pcb3 pcbc.txt pcb 3 pcbd pcb4 pcbd.txt pcb 4 > aa=read.AgilentFE(targets, makePLOT=FALSE) Read conta.txt Read contb.txt Read contc.txt Read contd.txt Read pcba.txt Read pcbb.txt Read pcbc.txt Read pcbd.txt RGList: dd$R: 'gProcessedSignal' dd$G: 'gMeanSignal' dd$Rb: 'gBGMedianSignal' dd$Gb: 'gBGUsed' > aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE) BACKGROUND CORRECTION AND NORMALIZATION foreground: MeanSignal background: BGMedianSignal BGmethod: half NORMmethod: quantile OUTPUT in log-2 scale ------------------------------------------------------ > aaFILT = filter.probes(aaNORM, control = TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG= TRUE, sat=TRUE, PopnOL = TRUE, NonUnifOL = TRUE, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = F, annotation.package = "org.Dr.eg.db", flag.counts = TRUE, targets) FILTERING PROBES BY FLAGS Error in filter.probes(aaNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE, : 'targets' is missing Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607 [[alternative HTML version deleted]]
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Hi Neel, you want to have "targets=targets)" at the end of your call to filter.probes. Otherwise it thinks that targets is the value for for the limSAT argument. If you're not going to follow the order of arguments, you should make sure to name every argument in the function. Francois On 12/09/2009 06:56 PM, Neel Aluru wrote: > Hello, > > Can anyone help me in troubleshooting the function for filtering probes. Below is the session info and I am just trying the functions in the user guide. > Thank you, > > Neel > > Session info. > >> setwd("/Users/Neel/agilent") >> library("Agi4x44PreProcess") >> targets=read.targets(infile="infile.txt") > > Target File > X FileName Treatment GErep > conta cont1 conta.txt control 1 > contb cont2 contb.txt control 2 > contc cont3 contc.txt control 3 > contd cont4 contd.txt control 4 > pcba pcb1 pcba.txt pcb 1 > pcbb pcb2 pcbb.txt pcb 2 > pcbc pcb3 pcbc.txt pcb 3 > pcbd pcb4 pcbd.txt pcb 4 > >> aa=read.AgilentFE(targets, makePLOT=FALSE) > Read conta.txt > Read contb.txt > Read contc.txt > Read contd.txt > Read pcba.txt > Read pcbb.txt > Read pcbc.txt > Read pcbd.txt > > RGList: > dd$R: 'gProcessedSignal' > dd$G: 'gMeanSignal' > dd$Rb: 'gBGMedianSignal' > dd$Gb: 'gBGUsed' > >> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE) > BACKGROUND CORRECTION AND NORMALIZATION > > foreground: MeanSignal > background: BGMedianSignal > > BGmethod: half > NORMmethod: quantile > OUTPUT in log-2 scale > > ------------------------------------------------------ >> aaFILT = filter.probes(aaNORM, control = TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG= TRUE, sat=TRUE, PopnOL = TRUE, NonUnifOL = TRUE, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = F, annotation.package = "org.Dr.eg.db", flag.counts = TRUE, targets) > FILTERING PROBES BY FLAGS > > Error in filter.probes(aaNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE, : > 'targets' is missing > > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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