Howdy folks. I am trying to run some QC on a set of single channel agilent
microarray files and would like to generate MA plots for them, but since
they are single channel, plotMA3by2 doesn't appear to work(see error below).
Could I be missing something? or is there an simple alternate method that
could generate MA plots? Any suggestions folks have is muchly appreciated.
-Rich

I managed to load my array data successfully:

RG <-
read.maimages(files=dir(),source="agilent",columns=list(G="gMeanSignal",Gb="gBGMedianSignal",R="gMeanSignal",Rb="gBGMedianSignal"))

And successfully performed back ground correction and normalization on the
data


RG2 <- backgroundCorrect(RG, method="normexp", offset=50)

RG2 <- normalizeBetweenArrays(RG2$G, method="quantile")

RG2 <- log(RG2)

plotMA3by2(RG2, device="pdf")
This produces the following error:

> plotMA3by2(RG2, device="pdf")
Error in MA$weights : $ operator is invalid for atomic vectors
Calls: plotMA3by2
Execution halted

I have managed to successfully generate a box plot and a HCA on the
normalized data.

Thanks again!

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