[BioC] How to use detect call in GCRMA (or RMA) analysis?

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Thu Dec 7 05:54:30 CET 2006

On Dec 6, 2006, at 2:47 PM, Wang mingyi wrote:

> Dear all,
> I have a question for Affymetrix data analysis by GCRMA (or RMA).  
> From the GCRMA (RMA) results, we cannot get detect call information  
> which can be returned from MAS5. I think this information are  
> useful when we want to perform some downstream t-tests. For  
> example, three replicates (after drug) comparing with other three  
> replicates (before drug), if given one gene, most detect values are  
> "A" in all these 6 replicates, we will think the t-test doesnot  
> make sense. So how to deal with this situation? Can we incorporate  
> with detect call information from MAS5?
> Thank you in advance!

GCRMA or RMA does not make presence/absence calls like MAS5 does. One  
way to deal with this is to do the relevant routine and then  
subsequently remove the probesets which are declared absent using  
MAS5. You could also remove them before doing RMA/GCRMA but that is a  
bit harder.


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