To clarify, what you suggested worked perfectly! On Jun 30, 2010, at 3:36 PM, Richard Friedman wrote: > Pedro, > > I just got back to the microRNA today. > Thank you very much! > > Best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > George Scithers > > > > On Jun 21, 2010, at 5:04 AM, Pedro L?pez Romero wrote: > >> Hi Neel and Richard, >> >> Thanks for your patience. >> >> >> >> I have slitghtly modified some code in the package, basically >> related to the way read.maimages is used. I have eliminated the use >> of the "chr_coord" column in some of the output files which it was >> what it was causing problems. Before these changes are made >> effective in the library, please, try this temporal solution: >> >> >> >> dd=read.maimages(files=targets$FileName,source="agilent", >> >> columns=list(Rf="gTotalGeneSignal", >> >> >> Gf="gTotalProbeSignal", >> >> >> Rb="gMeanSignal", >> >> >> Gb="gProcessedSignal"), >> >> >> other.columns=list(IsGeneDetected="gIsGeneDetected", >> >> IsSaturated >> ="gIsSaturated", >> >> IsFeatNonUnifOF >> ="gIsFeatNonUnifOL", >> >> IsFeatPopnOL >> ="gIsFeatPopnOL", >> >> >> probe_mappings="probe_mappings", >> >> BGKmd >> ="gBGMedianSignal", >> >> BGKus >> ="gBGUsed"), >> >> annotation = c( "ControlType", >> "ProbeName","GeneName"), >> >> verbose=TRUE,sep="\t",quote="") >> >> >> >> >> >> before doing anything else, please check first that you have >> "probe_mappings" in the fifth position of "dd$other" >> >>> names(dd$other)[5] >> >> [1] "probe_mappings" >> >> >> >> Then, change the name of "probe_mappings" to the name that >> AgiMicroRna uses for this variable: >> >>> names(dd$other)[5] = "chr_coord" >> >> >> >> Then, use the rest of the functions as usual: >> >> >> >> ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) >> >> ddPROC = filterMicroRna(ddTGS.rma, >> >> dd, >> >> control = TRUE, >> >> IsGeneDetected = TRUE, >> >> wellaboveNEG = FALSE, >> >> limIsGeneDetected = 50, >> >> limNEG = 25, >> >> makePLOT = FALSE, >> >> targets, >> >> verbose = TRUE) >> >> >> >> >> >> Please, let me know if you still have any problem. Thanks >> >> >> >> p.- >> >> >> >> >> >> De: Neel Aluru [mailto:naluru at whoi.edu] >> Enviado el: Friday, June 18, 2010 1:44 PM >> Para: Pedro L?pez Romero; bio c bioconductor >> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse >> miRNA Microarray Release 12.0 G4471A-021828. >> >> >> >> Thanks, Pedro. Looking forward to hearing from you. >> >> Sincerely, >> Neel >> >> At 03:20 AM 6/18/2010, Pedro L?pez Romero wrote: >> >> >> >> Thanks Neel, >> >> I am working on your data, I know where the problem is. I have to >> modify (or even write a new function) to read the data in such a >> way that it is more flexible to the different data formats. I will >> let you know when I have this ready. >> >> p.- >> >> De: Neel Aluru [ mailto:naluru at whoi.edu <mailto:naluru at="" whoi.edu=""> ] >> Enviado el: Thursday, June 17, 2010 1:49 PM >> Para: Pedro L?pez Romero; bio c bioconductor >> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse >> miRNA Microarray Release 12.0 G4471A-021828. >> >> Thanks, Pedro. >> >> Here are the details you. I have noticed that what is in dd$genes >> and dd$other is different depending on whether I use read.maimages >> or readMicroRnaAFE function. I have pasted the details from both of >> them. >> >> The feature extraction software I used was version 9.3. >> >> Sincerely, >> Neel >> >> Session info () using read.maimages function >> >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="targets.txt", verbose=TRUE) >> >> Target File >> FileName Treatment GErep Subject >> 36_DMSO_1 36_DMSO_1.txt 36DMSO 1 1 >> 36_DMSO_2 36_DMSO_2.txt 36DMSO 1 2 >> 36_DMSO_3 36_DMSO_3.txt 36DMSO 1 3 >> 36_TCDD_1 36_TCDD_1.txt 36TCDD 2 1 >> 36_TCDD_2 36_TCDD_2.txt 36TCDD 2 2 >> 36_TCDD_3 36_TCDD_3.txt 36TCDD 2 3 >> 60_DMSO_1 60_DMSO_1.txt 60DMSO 3 1 >> 60_DMSO_2 60_DMSO_2.txt 60DMSO 3 2 >> 60_DMSO_3 60_DMSO_3.txt 60DMSO 3 3 >> 60_TCDD_1 60_TCDD_1.txt 60TCDD 4 1 >> 60_TCDD_2 60_TCDD_2.txt 60TCDD 4 2 >> 60_TCDD_3 60_TCDD_3.txt 60TCDD 4 3 >> >>> ddaux=read.maimages(files=targets.micro$FileName,source="agilent", >> + other.columns=list(IsGeneDetected="gIsGeneDetected", >> + IsSaturated="gIsSaturated", >> + IsFeatNonUnifOF="gIsFeatNonUnifOL", >> + IsFeatPopnOL="gIsFeatPopnOL", >> + ChrCoord="chr_coord", BGKmd="gBGMedianSignal", >> + BGKus="gBGUsed"), >> + columns=list(Rf="gTotalGeneSignal", >> + Gf="gTotalProbeSignal", >> + Rb="gMeanSignal",Gb="gProcessedSignal"), >> verbose=TRUE,sep="\t",quote="") >> Read 36_DMSO_1.txt >> Read 36_DMSO_2.txt >> Read 36_DMSO_3.txt >> Read 36_TCDD_1.txt >> Read 36_TCDD_2.txt >> Read 36_TCDD_3.txt >> Read 60_DMSO_1.txt >> Read 60_DMSO_2.txt >> Read 60_DMSO_3.txt >> Read 60_TCDD_1.txt >> Read 60_TCDD_2.txt >> Read 60_TCDD_3.txt >>> names(ddaux) >> [1] "R" "G" "Rb" "Gb" "targets" "genes" >> "source" >> [8] "other" >>> names(ddaux$genes) >> [1] "Row" "Col" "Start" "Sequence" >> [5] "ProbeUID" "ControlType" "ProbeName" "GeneName" >> [9] "SystematicName" "Description" >>> names(ddaux$other) >> [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" >> "gIsFeatPopnOL" >> [5] "gBGMedianSignal" "gBGUsed" >> >> Session Info () with AgiMicroRnaAFE function. >> >>> ddaux=readAgiMicroRnaAFE(targets.micro, verbose=TRUE) >> Error: could not find function "readAgiMicroRnaAFE" >>> ddaux=readMicroRnaAFE(targets.micro, verbose=TRUE) >> Read 36_DMSO_1.txt >> Read 36_DMSO_2.txt >> Read 36_DMSO_3.txt >> Read 36_TCDD_1.txt >> Read 36_TCDD_2.txt >> Read 36_TCDD_3.txt >> Read 60_DMSO_1.txt >> Read 60_DMSO_2.txt >> Read 60_DMSO_3.txt >> Read 60_TCDD_1.txt >> Read 60_TCDD_2.txt >> Read 60_TCDD_3.txt >> >> RGList: >> dd$R: 'gTotalGeneSignal' >> dd$G: 'gTotalProbeSignal' >> dd$Rb: 'gMeanSignal' >> dd$Gb: 'gProcessedSignal' >> >>> names(ddaux) >> [1] "R" "G" "Rb" "Gb" "targets" "genes" >> "other" >>> names(ddaux$genes) >> [1] "Sequence" "ProbeUID" "ControlType" >>> names(ddaux$other) >> [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" >> "gIsFeatPopnOL" >> [5] "gBGMedianSignal" "gBGUsed" >> >> >> >> At 04:29 AM 6/17/2010, Pedro L?pez Romero wrote: >> >> Hi Neel, >> >> I think your problem with the filtering function, is not the >> filtering itself but when the function tries to write an output. I >> am modifying this, so the user can choose whether or not they want >> to have an output file in the filtering step. In the meantime, can >> you tell me what you have in? >> names(dd), >> names(dd$genes) >> names(dd$genes) >> names(dd$other) >> >> What version of the Extractor are you using? >> >> >> >> p.- >> >> De: Neel Aluru [ <mailto:naluru at="" whoi.edu=""> mailto:naluru at whoi.edu] >> Enviado el: Wednesday, June 16, 2010 10:54 PM >> Para: Richard Friedman; Pedro L?pez Romero; bio c bioconductor >> Asunto: Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse >> miRNA Microarray Release 12.0 G4471A-021828. >> >> Hi Rich, >> >> Did you try filtering probes using FilterMicroRna function after >> removing the two columns. I am having difficulty in filtering probes. >> >> Thanks, >> Neel >> >> At 04:19 PM 6/16/2010, Richard Friedman wrote: >> >> Dear Pedro and List, >> >> My text files form Agilent Mouse miRNA Microarray Release 12.0 >> G4471A-021828 has two extra columns which are not >> in GSE19232 Agilent human microRNA array v 2.0 (G44708) - "start" >> and "sequence". When these are deleted >> AgiMicroRNA works. I do not know if this is due to the array or >> software or processing options on the software. >> This clears up the problem with maMicroRna( which i have been writing >> you about. It would be nice if >> this could be taken into automatically in a future version of >> AgiMicroRNA, but this solves my porblem for now. >> >> Thanks and best wishes, >> Rich >> ------------------------------------------------------------ >> Richard A. Friedman, PhD >> Associate Research Scientist, >> Biomedical Informatics Shared Resource >> Herbert Irving Comprehensive Cancer Center (HICCC) >> Lecturer, >> Department of Biomedical Informatics (DBMI) >> Educational Coordinator, >> Center for Computational Biology and Bioinformatics (C2B2)/ >> National Center for Multiscale Analysis of Genomic Networks (MAGNet) >> Room 824 >> Irving Cancer Research Center >> Columbia University >> 1130 St. Nicholas Ave >> New York, NY 10032 >> (212)851-4765 (voice) >> friedman at cancercenter.columbia.edu >> http://cancercenter.columbia.edu/~friedman/ >> >> In Memoriam, >> George Scithers >> >> _______________________________________________ >> 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 >> >> Neel Aluru Ph.D. >> Post doctoral Scholar >> Biology Department >> Redfield 304 (MS#32) >> Woods Hole Oceanographic Institution >> Woods Hole MA 02543 USA >> Phone: (508) 289-3607 [Office] >> 774-392-3727 [Cell] >> RID: A-7237-2009 >> >> ________________________________ >> >> *************** AVISO LEGAL *************** >> Este mensaje va dirigido, de manera exclusiva, a su destinatario y >> contiene informaci?n confidencial y sujeta al secreto profesional, >> cuya divulgaci?n no est? permitida por la ley. 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Si no consintiese la utilizaci?n del correo >> electr?nico o de las comunicaciones v?a Internet le rogamos nos lo >> comunique y ponga en nuestro conocimiento de manera inmediata. >> >> ________________________________ >> >> *************** LEGAL NOTICE ************** >> This message is intended exclusively for the person to whom it is >> addressed and contains privileged and confidential information >> protected from disclosure by law. If you are not the addressee >> indicated in this message, you should immediately delete it and any >> attachments and notify the sender by reply e-mail or by phone (+34 >> 914531200). In such case, you are hereby notified that any >> dissemination, distribution, copying or use of this message or any >> attachments, for any purpose, is strictly prohibited by law. 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Si no consintiese la utilizaci?n del correo >> electr?nico o de las comunicaciones v?a Internet le rogamos nos lo >> comunique y ponga en nuestro conocimiento de manera inmediata. >> >> ________________________________ >> >> *************** LEGAL NOTICE ************** >> This message is intended exclusively for the person to whom it is >> addressed and contains privileged and confidential information >> protected from disclosure by law. If you are not the addressee >> indicated in this message, you should immediately delete it and any >> attachments and notify the sender by reply e-mail or by phone (+34 >> 914531200). In such case, you are hereby notified that any >> dissemination, distribution, copying or use of this message or any >> attachments, for any purpose, is strictly prohibited by law. We >> hereby inform you, as addressee of this message, that e-mail and >> Internet do not guarantee the confidentiality, nor the completeness >> or proper reception of the messages sent and, thus, CNIC does not >> assume any liability for those circumstances. Should you not agree >> to the use of e-mail or to communications via Internet, you are >> kindly requested to notify us immediately. >> >> Neel Aluru Ph.D. >> Post doctoral Scholar >> Biology Department >> Redfield 304 (MS#32) >> Woods Hole Oceanographic Institution >> Woods Hole MA 02543 USA >> Phone: (508) 289-3607 [Office] >> 774-392-3727 [Cell] >> RID: A-7237-2009 >> >> >> >> >> *************** AVISO LEGAL *************** >> >> Este mensaje va dirigido, de manera exclusiva, a su destinatario y >> >> contiene informaci?n confidencial y sujeta al secreto profesional, >> >> cuya divulgaci?n no est? permitida por la ley. 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