[BioC] Intensity based filtering

morten.mattingsdal at student.uib.no morten.mattingsdal at student.uib.no
Sat Nov 13 18:03:17 CET 2004

> 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

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

tmp1G <- RG$G
tmp1R <- RG$R
ctmp1G <- tmp1G
RG$R <-tmp1R
RG$G <- tmp1G
#Replaces values under 200 or over 65000 in BOTH channels with value NA.


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