Thanks, Pedro. Looking forward to hearing from you. Sincerely, Neel At 03:20 AM 6/18/2010, Pedro López 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@whoi.edu] >Enviado el: Thursday, June 17, 2010 1:49 PM >Para: Pedro López 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$other) >[1] >"gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" "gIsFeatPopnOL" >[5] "gBGMedianSignal" "gBGUsed" > > > >At 04:29 AM 6/17/2010, Pedro López Romero wrote: > >Hi Neel, > >I think your problem with the filtering >function, is not the filtering itself but when >the function tries to write an output. I am >modifying this, so the user can choose whether >or not they want to have an output file in the >filtering step. In the meantime, can you tell me what you have in? >names(dd), >names(dd$genes) >names(dd$genes) >names(dd$other) > >What version of the Extractor are you using? > > > >p.- > >De: Neel Aluru [ mailto:naluru@whoi.edu] >Enviado el: Wednesday, June 16, 2010 10:54 PM >Para: Richard Friedman; Pedro López 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@cancercenter.columbia.edu >http://cancercenter.columbia.edu/~friedman/ > >In Memoriam, >George Scithers > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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 información >confidencial y sujeta al secreto profesional, >cuya divulgación no está permitida por la ley. >En caso de haber recibido este mensaje por >error, le rogamos que, de forma inmediata, nos >lo comunique mediante correo electrónico >remitido a nuestra atención o a través del >teléfono (+34 914531200) y proceda a su >eliminación, así como a la de cualquier >documento adjunto al mismo. 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Asimismo, le >comunicamos que la distribución, copia o >utilización de este mensaje, o de cualquier >documento adjunto al mismo, cualquiera que fuera >su finalidad, están prohibidas por la ley. Le >informamos, como destinatario de este mensaje, >que el correo electrónico y las comunicaciones >por medio de Internet no permiten asegurar ni >garantizar la confidencialidad de los mensajes >transmitidos, así como tampoco su integridad o >su correcta recepción, por lo que el CNIC no >asume responsabilidad alguna por tales >circunstancias. Si no consintiese la utilización >del correo electrónico o de las comunicaciones >vía 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 [[alternative HTML version deleted]]