[BioC] Fold Change values after RMA

[James W. MacDonald]

Hi David,

kfbargad at ehu.es wrote:
> Dear List,
> 
> I have come across an article (Choudary et al. 2005, PNAS 102,15653-
> 15658) where they state that the FC values after RMA 
> preprocessing "always" remain below a maximum of 2.0 Is this right?

No, this is not correct. There are other factual errors in that paper as 
well, which makes me wonder if there was a breakdown in communication 
between the statisticians and those who wrote the paper.

That said, it is my understanding that fold change values in brain are 
often very small, so they may simply be trying to indicate that using a 
fold change of two is not reasonable in that context.

Best,

Jim


> 
> I have performed some analyses using RMA, quantile normalisation and 
> limma and am getting M values higher than 2, and if M = log2(FC), then 
> FC values are higher than 4. What am I missing? Any comments on this?
> 
> Thanks in advance,
> 
> David
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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