[BioC] limma question

[Thomas Schlitt]

Hi
I am working with a chip which contains "empty" spots, i.e. nothing has been
spotted there, "landing lights", and actual spots "cDNA". I would like to
exclude "empty" and "landing light" spots from my dataset before
normalisation.

So, this works fine:
library(limma)
targets=readTargets(...)
spottypes=readSpotTypes(...)
files = c(targets$FileNameCy3, targets$FileNameCy5)
numrows = length(files)/2
dim(files) = c(numrows,2)
rawdata = read.imagene(files, path=...)
g2=data.frame(ID=rawdata$genes$"Gene ID",Name=rawdata$genes$"Gene ID")
status = controlStatus(spottypes,g2)
normdata = normalizeWithinArrays(rawdata)

... and I tried this to exclude the "empty" spots and "landing lights":

raw2=rawdata[status=="cDNA",]
normdata = normalizeWithinArrays(raw2,method="none")

... which works fine, but with

normdata = normalizeWithinArrays(raw2)

I get this
>Error: subscript out of bounds

Any suggestions?

Thanks
Thomas

_________________________
Thomas Schlitt
British Antarctic Survey
th_schlitt at gmx.de

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