[BioC] A question about MAS5 vs RMA vs GCRMA

YUK FAI LEUNG yfleung at mcb.harvard.edu
Mon Sep 13 17:40:25 CEST 2004


Adai,

Thanks! I did not notice that. I have never used MAS5 in Bioc. After 
correcting for this error, and using the P calls, the number of genes >= 
2 fold equals to 147.

Best regards,
Fai



Adaikalavan Ramasamy wrote:

> 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
> 
> 
> 

-- 
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
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