Hi John, I might be missing what you mean ... To read microarray data in a generic format, you have to tell limma the column names of the data columns you want it to read. This means that you have to check first yourself, eg using Excel or a text editor, to see what column headings the files contain. Given a generic format file, limma simply finds the first line in the file which contains the required column names, skipping any earlier lines, and reads from there. Best wishes Gordon On Thu, 25 Jun 2009, john seers (IFR) wrote: > Hi > > Just out of curiosity, how does limma know how to match the names? Where > do the column names come from? > > I am missing something here ... > > Regards > > > John > > > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon K > Smyth > Sent: 25 June 2009 08:09 > To: Juana Arco > Cc: Bioconductor mailing list > Subject: [BioC] Limma - GenePix > > Dear Juana, > > Once the file has been processed by ArrayExpress, and the header > removed, > the file is no longer a valid GPR format file. You therefore use > format="generic" and supply the column names, just as you've done. I > expect what you give below will work, but you can easily confirm by > trying > it. > > Best wishes > Gordon > ne.science.biology.informatics.conductor >

Yes, exactly. By file header, I mean the information read by readGPRHeader(). Gordon On Thu, 25 Jun 2009, john seers (IFR) wrote: > > Hi All > > Ah!. Perhaps, "the header removed" does not mean removing the header > row. Just the n lines of Genepix information? > > > > Regards > > > John > > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon K > Smyth > Sent: 25 June 2009 08:09 > To: Juana Arco > Cc: Bioconductor mailing list > Subject: [BioC] Limma - GenePix > > Dear Juana, > > Once the file has been processed by ArrayExpress, and the header > removed, > the file is no longer a valid GPR format file. You therefore use > format="generic" and supply the column names, just as you've done. I > expect what you give below will work, but you can easily confirm by > trying > it. > > Best wishes > Gordon > >> Date: Tue, 23 Jun 2009 13:53:19 +0000 >> From: Juana Arco <luana_arch at="" hotmail.com=""> >> Subject: [BioC] Limma - GenePix >> To: <bioconductor at="" stat.math.ethz.ch=""> >> Message-ID: <snt109-w62ce4e25ce69389a9bf63eff360 at="" phx.gbl=""> >> Content-Type: text/plain >> >> Hi, >> Can >> anybody help me with this? >> 1) >> I've >> downloaded from the ArrayExpress some GenePix files that don't have >> headers. Because of that I had to read the files (.txt extension for >> some reason) this way: >> >> RG <- >> read.maimages(targets$Filename, columns=list(Rf="GenePix:F635 >> Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635 >> Median",Gb="GenePix:B532 Median"), sep="\t", >> path="./") >> >> Is this correct? >> >> 2) I had to >> create the targets files from a file provided by arrayexpress which >> looked something like this: >> >> >> >> SlideNumber Source >> Name Label FileName >> 1 8CT Cy5 1348628744.txt >> 2 5Exp Cy3 1348628729.txt >> 3 10Exp Cy5 1348628754.txt >> 4 4CT Cy3 1348628724.txt >> 5 1Exp Cy5 1348628709.txt >> 6 12Exp Cy5 1348628764.txt >> 7 6Exp Cy5 1348628734.txt >> 8 3CT Cy3 1348628719.txt >> 9 13Exp Cy3 1348628769.txt >> 10 7Exp Cy3 1348628739.txt >> 11 2CT Cy5 1348628714.txt >> 12 11Exp Cy3 1348628759.txt >> 13 9Exp Cy5 1348628749.txt >> 14 14CT Cy3 1348628774.txt >> >> >> >> And >> my target file looks like this >> >> >> >> SlideNumber Filename Cy3 Cy5 >> 1 1348628744.txt case control >> 2 1348628729.txt case control >> 3 1348628754.txt control case >> 4 1348628724.txt control case >> 5 1348628709.txt control case >> 6 1348628764.txt control case >> 7 1348628734.txt control case >> 8 1348628719.txt control case >> 9 1348628769.txt case control >> 10 1348628739.txt case control >> 11 1348628714.txt case control >> 12 1348628759.txt case control >> 13 1348628749.txt control case >> 14 1348628774.txt control case >> >> Is >> this correct? >> Luana > > _______________________________________________ > 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 >