To whom it may concern,
I'm analyzing some Affy human exon array data and hope to generate similar
plots as seen in the supplementary figures in the Purdom 2008 Bioinformatics
paper. To do so, I need to get the normalized probe intensities and
residuals.
I've already followed the steps described in the Human Exon Array Analysis
vignette and get the following:
(1) ...
csN <- process(qn, verbose=verbose)
(2) ...
res<-getResidualSet(plmTr)
I tried the function "extractDataFrame(...,addNames=TRUE)" hoping to get the
data plus column labels for my samples but it didn't work. Is there any
easy way to extract these two sets of data in matrix format similar to the
FIRMA score matrix with probe ID and column labels?
Thanks,
Jing
Jing Ma
Hartwell Center for Bioinformatics & Biotechnology
St. Jude Children's Research Hospital
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