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

Rafael Irizarry ririzarr at jhsph.edu
Tue Jun 22 02:48:58 CEST 2004

rma sacrifices accuracy for its gains in precission. this has two 

1- for a fixed false positive rate, RMA tends to have many more true 
2- to attain the same true positive rate as with mas 5.0 you need to 
lower the fold-change cut-off (which is arbitrary anyway). e.g. if you 
are using fold change>2 as your cut-off and RMA gives lists that you 
think are too small,  then use fold change > 1.5.

this has more to do with background correction than normalization. it 
is discussed in some detail in the gcrma paper appearing in JASA soon;


On Jun 21, 2004, at 5:35 PM, Adaikalavan Ramasamy wrote:

> 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
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