[BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis

[Michal Okoniewski]

Hi Dan,
> You can use also the CDFs from X:MAP downloads page - they manage with 
> RMA/plier.
>
> I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB 
> SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A 
> FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'.
>
> Cheers,
> Dan
The cdf available at X:MAP page does not in fact require the whole X:MAP 
database to run. You can use read.exon(),
attach the CDF to the AffyBatch, call RMA/plier and do pairwise 
comparison without connecting to the DB - you'll get eSet with the vast 
majority of Affy exon probesets.

However all the other functionality of exonmap: annotation translating, 
filtering, visualization - do a lot of X:MAP queries in mysql.
This functionality you can also use on the data processed with other 
packages (eg xps) or imported from outside.

My hint for doing data mining with exon arrays is to use in parallel: 
exonmap and X:MAP browser and perhaps sometimes Ensembl and other 
databases to see transcripts, isoforms and exons and their expression 
profiles. But this is at the stage of "deeper insight" after the 
summarization and filtering.

The other questions have been answered already by Christian and Jim :)  
Thanks!

Best,
Michal