[BioC] A question about MAS5 vs RMA vs GCRMA

[Adaikalavan Ramasamy]

In BioConductor, the rma and gcrma expression measures are log2
transformed while MAS 5.0 is not. Could this be your reason ?

Regards, Adai


On Mon, 2004-09-13 at 15:48, YUK FAI LEUNG wrote:
> Hi there,
> 
> I am helping my friend to do some analysis on his affy data. He has a 
> simple 2x2 factorial experiment without any replication, i.e. only 4 
> chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw 
> data with the default settings, and compute the fold changes of 
> individual factor comparison. I am suprised to see that there are many 
> more genes which have >= 2 fold change in MAS5 compare to the other two 
> algorithms. For example in one comparison, MAS5 gives 21477 genes >= 2 
> fold, while RMA gives 0 and GCRMA gives 4.
> 
> While I do know that RMA gives less significant genes, I do not expect 
> to see such a drastic difference. Especially when his experiment is a 
> drug treatment on a cell culture which is known to change a lot of 
> genes, I am expecting to see a lot of changes even in the fold change 
> comparison. Is this discrepancy occured due to the lack of replication?
> 
> Regards,
> Fai