> Date: Fri, 17 Jun 2005 08:46:20 -0700 (PDT) > From: Bogdan Terletskiy <terbogdan at="" yahoo.com=""> > Subject: [BioC] GenePix files .mrg > To: bioconductor at stat.math.ethz.ch > > Hi > > I try to analyze our cDNA microarray data by limma package. I have encountered problem with files > loading to the R workspace. > > The problem is with file format. All experiments were made on 13K chicken cDNA at Fred Hutchison > Cancer Research Center. Results of scanning were transformed to tab delimited files by using > GenePix program, but output format of all this files are *.mrg but not .gpr . These files have all > Genepix attributes, and similar general features (for example, the cap of table have following > looks: > > BlockColumnRowNameIdDiamF635MedianF635MeanF635SDB635MedianB635MeanB 635SDF532MedianF532MeanF532SDB532MedianB532MeanB532SDRatioOfMediansLog RatioF635MedianMnB635F532 > MedianMnB532GprFlagsSourceSource Clone NamePCR Amp CodeSource Assigned AnnotationTIGR: GB > AccessionTIGR: EST IdTIGR: TCTIGR: AnnotationBLAST AnnotationComment > > But I couldn?t import them to R limma workspace by typical > > RG <- read.maimages(targets$FileName, source="genepix") or > > RG <- read.maimages(files, columns=list(Rf="F635 Mean",Gf="F532 Mean",Rb="B635 Median",Gb="B532 > Median")) > > Can I work with such file format using limma , or should I require classical .gpr files from > FHCRC? GPR is the only GenePix results file format which is documented by the GenePix people, see http://www.axon.com/gn_GenePix_File_Formats.html We don't know anything about the mrg file format. We can only support publicly documented formats. Gordon > Thanks in advance, > Sincerely youth Dr. Bogdan Terletskyi