[BioC] Affy EXON Array: iterPLIER or RMA

Daniel Brewer daniel.brewer at icr.ac.uk
Tue May 8 11:25:56 CEST 2007

Crispin Miller wrote:
> 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

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.

Many thanks


Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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