[BioC] GenePix files .mrg

Gordon K Smyth smyth at wehi.EDU.AU
Sun Jun 19 14:06:04 CEST 2005

> 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:
>  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

GPR is the only GenePix results file format which is documented by the GenePix people, see


We don't know anything about the mrg file format.  We can only support publicly documented formats.


> Thanks in advance,
> Sincerely youth Dr. Bogdan Terletskyi

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