[BioC] Affy EXON Array: iterPLIER or RMA

[Michal Okoniewski]

Hi Jim and Daniel, 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W.
MacDonald
Sent: 08 May 2007 17:44


Daniel Brewer wrote:
> I did look into exonmap, but was scared off by the memory (mainly) and

> setup requirements.  Is it possible to use APT (affymetrix power 
> tools) to produce the exon-level summaries and then use the exonmap 
> package for the annotation and analysis?  The advantages to using APT 
> is that it uses memory efficient techniques in C++ unlike R.

I suppose you could, but that sort of misses the whole point of the
exonmap package, which I think is to be able to choose which probesets
you want to use when computing an expression value for a particular
gene.

The annotation will probably not be much different from what you get
using Affy's software (at the level of expression values for a set of
probesets), so in this instance I don't know if you gain much for the
outlay of time.

Best,

Jim
=============

Finding right probesets for a gene-level summary - as Jim wrote - 
is one of the possible and important uses of exonmap. 

However - it is also possible (as Daniel suggests) - to get ready
numbers
from APT (or its derivatives - ExACT or expression console), import it 
into R via a flat file and use exonmap just to process
gene/transcript/exon/probeset annotations. I was doing it myself happily
a couple of times. 

As for annotations in XMAP database (so in exonmap) - they are
genome-based
and independent from Affy - thus you can get for example more detailed
information 
on genome multiple targeting (ie. cross-hybridization).

Cheers, 
Michal
 
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