[BioC] RMA vs VSN

[peter robinson]

On Monday 21 June 2004 21:08, Roger Vallejo wrote:
> This must be of interest for those preprocessing data from affymetrix
> chips. We have compared RMA vs VSN performing an lme-ANOVA. If you are
> wondering what to use RMA or VSN? or what are the potential pitfalls or
> benefits from using either normalization or background data correction
> approach. Then, please read below and make your own conclusions.
>
>
>
> Thank you to the enlightening discussion followed up with colleagues at
> the Bioconductor group.
>


I'd like to throw another observation with request for comments into this 
round. Our group has been using affymetrix murine chips with pooled samples 
but no technical replicates as a way of identifying candidate genes for 
further characterization by RT-PCR or in situ hybridization and other 
techniques. We have used a simple fold-change threshold between samples taken 
from different developmental stages or between wt and ko models to identify 
candidates.

Then, we are able to confirm about 80% of genes predicted following mas5 
analysis (original or bioconductor is very similar).
However, rma analysis has produced lists of genes that are much shorter and in 
general do not correspond well to the confirmed lists of genes produced by 
mas5 (or to our biological prejudices as to what genes should be observed).

Have others notices similar discrepancies between mas5 and rma?  Are there 
perhaps other issues I have overlooked?

Thanks

Peter