[BioC] ignore blanks in GPR

[Lourdes Peña Castillo]

Hi, 

What I do is to read everything, create a spottypes.txt file (limma
users guide pag. 12) to identify the lines in the GPR files according
to the Name or ID column, and then remove those which match certain
label.

For example (assume in the spottypes file you label "blank" the lines
with ID BLANK or '"), then you could do:

RG <- read.maimages(targets$Filename, 
        source = "genepix", 
        columns = columns) 
spottypes <- readSpotTypes()
RG$genes$Status<-controlStatus(spottypes,RG)
RG <- RG[RG$genes$Status != "blank",]

Hope this helps,

Lourdes


> What I do is to read in everything and then give weight 0 to these lines.
> 
> --Naomi
> 
> At 12:27 PM 7/18/2005, Guoneng Zhong wrote:
> >Hi,
> >
> >In limma, how do I read a GPR file and ignore any lines whose ID column
> >is BLANK or ""?
> >
> >This is my line:
> >
> >RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F532
> >Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median"))
> >
> >Thanks!
> >G
> >
> >_______________________________________________
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> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111