[BioC] Probe-level analysis of exon arrays using xps

cstrato cstrato at aon.at
Thu Aug 18 20:28:54 CEST 2011

Dear Giovanni,

In principle you could do the background and normalization steps 
separately, e.g.:
 > data.bg.rma <- bgcorrect.rma(data.exon, ...)
 > data.qu.rma <- normalize.quantiles(data.bg.rma, ...)

Now you have the normalized probes, however, you cannot do any 
summarization such as median-polish or mean.

It is not quite clear to me how you want to proceed with the normalized 
probe intensities?

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 8/18/11 7:08 PM, Lavorgna Giovanni wrote:
> As you guys know, there is a growing evidence showing that a probe-level analysis  (as opposed to a probeset-level or a gene-level analysis) could be useful in analyzing Exon arrays. I am currently analyzing several human exon chips (185!) on a 4 GB machine and I am using the xps package. I would like to stick to this software since it allows to manage several chips with the resources at hand and I was wondering if anyone has ever tried to perform probe level analysis using xps. Also, I would be grateful if anyone could point out alternative resources to perform this job.
> Thanks in advance.
> Giovanni
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