[BioC] A question about MAS5 vs RMA vs GCRMA

[Martino Barenco]

Dear Fai,

I think justRMA() (If this is what you used) returns 2-log transformed 
values so that to >=2 fold changes correspond to (absolute 
difference)>=1 in that metric.

Bests

Martino

On Monday, September 13, 2004, at 03:48 PM, 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
> -- 
> Yuk Fai Leung
> Department of Molecular and Cellular Biology
> Harvard University
> BL 2079, 16 Divinity Avenue
> Cambridge, MA 02138
> Tel: 617-495-2599
> Fax: 617-496-3321
> email: yfleung at mcb.harvard.edu; yfleung at genomicshome.com
> URL: http://genomicshome.com
>
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>
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Martino Barenco
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