I've been running arrays (Affy mouse, Affy human) and RNAseq data (also
mouse and human) through UPC() for the past few days, after seeing some
nice results from the PNAS paper in comparison to qPCR and fRMA.  However,
I was hoping that the same aspect of the method which makes it useful for
RNAseq (i.e., decoupling background/foreground estimation from
platform-parameter estimation) would allow me to use it on Illumina array
data.  Has anyone tried this?

I can read in the appropriate bits (target sequence, length, GC content,
blah blah) for Illumina probes as if they were RNAseq data, or perhaps
assemble an oligo 'probedesign' package (less palatable) but I was hoping
someone else already bit the bullet.

Also, I wrote some patches to make the package work better with e.g. TCGA
RSEM data, where the count files have an initial header line.  (Obviously
this was trivial, but there was another interesting opportunity for
improvement so I hit that too)  Would be interested to hear from the
authors/maintainers regarding its utility.

Thanks,
--t



*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*

Benjamin Franklin, Poor Richard's
Almanack<http://archive.org/details/poorrichardsalma00franrich>

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