RMA vs. MAS 5.0 fold change compression (was Re: [BioC] RMA vs VSN)

[Adaikalavan Ramasamy]

I believe this is due to the fact that you have used Fold Change to
filter your gene list. Try filtering your genes by t-test or SAM and see
how the two lists compare.

In the last paragraph of the Results section of Irizarry et al, 2003
(Pubmed ID : 12582260), the authors mention that RMA compressed the Fold
Change estimates by 10-20%. This could be due to the quantile
normalisation. 

But in reality I often find 50-60% compression and am wondering why is
this myself. If anyone could shed light into this area, it would be much
appreciated. 


On Mon, 2004-06-21 at 11:39, peter robinson wrote:
<SNIP>
> 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