[BioC] Intensity based filtering

[morten.mattingsdal at student.uib.no]

> Hi All,
>
> How i filter based on intensity values (say lower
> limit 200 and upper limit 5000) for PM and MM for
> Affymetrix data? I have like 200 odd .CEL files, any
> ideas as to how to do this filtering for all these
> files in one go.
>
> Thanks,
> Hrishi

Hello Hrishi

This is how I use intensity based filtering with two-color .gpr files in
limma:

files <- dir(pattern="*\\.gpr$")
RG <- read.maimages(files,"genepix")

tmp1G <- RG$G
tmp1R <- RG$R
ctmp1G <- tmp1G
tmp1G[(tmp1G<200&tmp1R<200)|(tmp1G>65000&tmp1R>65000)]<-NA
tmp1R[(ctmp1G<200&tmp1R<200)|(ctmp1G>65000&tmp1R>65000)]<-NA
RG$R <-tmp1R
RG$G <- tmp1G
#Replaces values under 200 or over 65000 in BOTH channels with value NA.

morten