[BioC] Affy EXON Array: iterPLIER or RMA

[James W. MacDonald]

Hi Daniel,

Daniel Brewer wrote:
> Hi,
> 
> I am doing some analysis on the Affymetrix Exon human microarrays.
> Normally I would use RMA to summarize, but in the papers by Affymetrix
> they use iterPLIER for the gene-level estimates and PLIER for the
> Exon-level estimates.
> 
> Is it ok to use RMA for both summary levels for these arrays?
> Does anyone have an opinion on what the best approach to use is?

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).

Best,

Jim


> 
> Also does anyone use DABG to filter out badly detected probes?
> 
> Thanks
> 
> Daniel
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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