[BioC] Affy EXON Array: iterPLIER or RMA

[Crispin Miller]

Hi Daniel, Jim,

> Have you looked at the exonmap package?
>
> IIRC Affy intend iterPLIER to correct for the fact that lots of the
probesets on the exon array don't actually interrogate exons (according
to current 
> knowledge of the genome). In fact Wing Wong has recently published a
paper showing that the correlation between the 'core' 
> probesets and the 'full' and 'extended' are really bad.

> IMO, it is better to remove the probesets that we currently think are
either interrogating multiple transcripts or missing the exons
altogether _before_ > computing any expression values, so you don't have
to hope that the statistics are robust enough to ignore spurious signal.

> One downside to the exonmap package is the fact that you need a 64 bit
linux box with lots of RAM (which presumably you have already, else how
are you
> doing anything with these things?). In addition, you need to install
MySQL and set up the Ensembl core database, as well as the tables for
exonmap. 
> However, Michal and Crispin have given pretty detailed instructions
for how to go about doing that (I was able to get set up, and my
knowledge of DBs 
> wouldn't fill a thimble).

I'm not sure if this is your experience too?: we found we need a big
machine mainly for the normalization/expression summary side of things -
I don't think the package itself should need too much clout to manage
the annotation; it's the arrays themselves that eat up the RAM.

Cheers,

Crispin
 
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