[BioC] GenePix files .mrg

[Gordon K Smyth]

> 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
> 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