




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:

 BlockColumnRowNameIdDiamF635MedianF635MeanF635SDB635MedianB635MeanB635SDF532MedianF532MeanF532SDB532MedianB532MeanB532SDRatioOfMediansLogRatioF635MedianMnB635F532 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?

 

Thanks in advance,

Sincerely youth Dr. Bogdan Terletskyi 

 

 

 

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