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

[Dan Strumpf]

Hi Michal,

Thanks for your reply and suggestions! Please see my further 
comments/questions below in UPPER:

xps uses the "most proper" pgf and bkg Affymetrix annotation

SO THESE WOULD BE WHATEVER AFFYMETRIX IS PROVIDING - NOT REMAPPED FILES, 
CORRECT? IF YOU'RE FAMILIAR WITH XPS, COULD YOU INDICATE WHERE IN THE 
DOCUMENTATION THE INITIAL PROCESSING OF EXON ARRAYS (WITH REFERENCE TO 
THE USE OF PGF AND BKG) IS MENTIONED.

, while exonmap gives you
more flexibility of playing around with annotations

I REALIZE THAT XMAP HAS REMAPPED FILES

- both require extra database installation
effort, but I think it is worth it.

Did you run the summarization with this package?

I RUN THE COMPLETE RMA 'PROCESSING' SO THAT INCLUDED SUMMARIZATION.

I think the discussion in Oct 07 was about
the fact that you have to remove some probesets to run RMA... or was it 
fixed?

I COULD NOT TELL FROM THE COMMUNICATION IF THAT WAS FIXED. BECAUSE I HAD 
NO ISSUES RUNNING RMA USING THIS CDF PACKAGE, WOULD LIKE TO ASK IF THE 
AUTHOR OF huex10stv2cdf_1.15.0.tar.gz HAVE FIXED IT

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


Michal Okoniewski wrote:
> 
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf
> Sent: Mon 1/26/2009 10:17 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis
>  
> Hello,
> 
> I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz 
> package (downloaded from 
> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz
> )as a cdf source/mapping for processing Human exon array data within 'affy' 
> package. Processing went smoothly without any error messages. Noticed some 
> communication about this package in Oct. 2007, and am not clear if results 
> using it are relaible.
> I am interested in processing Human exon array data also with gcRMA and am 
> wondering if should use the above package or use xps/exonmap/oligo instead? 
> Would like to know also what are to options for differential expression 
> analysis equivalent to samr limma or RankProd for paired samples from within 
> exon array analysis packages or could the preprocessed/normalized data be 
> exported and used with xps/exonmap/oligo packages.
> 
> Thanks,
> 
> Dan
> =====================================================
> 
> Hi Dan,
> 
> xps uses the "most proper" pgf and bkg Affymetrix annotation, while exonmap gives you
> more flexibility of playing around with annotations - both require extra database installation
> effort, but I think it is worth it.
> 
> Did you run the summarization with this package? I think the discussion in Oct 07 was about
> the fact that you have to remove some probesets to run RMA... or was it fixed?
> You can use also the CDFs from X:MAP downloads page - they manage with RMA/plier.
> 
> Cheers,
> Michal 
>