[BioC] expression call

[James W. MacDonald]

Hi Galina,

Glazko, Galina wrote:
> Dear list
> 
>  
> 
> I need to select genes which are actually expressed in a set of Affy
> chips.
> 
> I've heard about 'expression call' thing, but I do not know exactly
> whether it is relevant to my problem.

I think you mean 'present call', which measures whether or not the 
intensities of PM probes for a particular probeset are significantly 
different from the corresponding MM probes. This is based on the idea 
that MM probes measure background binding, so if the PM probes are 
different, the transcript is assumed to be present (or expressed).

You can get these values by using the mas5calls() function in the affy 
package. See ?mas5calls for more information.

Best,

Jim


> 
> Would someone help me to solve it?
> 
>  
> 
> Best regards
> 
> Galina
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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