[BioC] AFFYMETRIX MISMATCH

[James W. MacDonald]

Marta Agudo wrote:
> Hi
> I´ve done an array experiment using Affymetrix arrays  and I was quite happy
> with the analysis (GCRMA) till the other day. A guy in a meeting told me
> that Affy chips have all these controls  which I thought were great, but he
> insisted that the mismatch-probes are more a pain than a good idea. He
> suggested I should re-analyse the arrays without the mismatched-results.
> Here is the question, what do you think? and if you agree, does any of you
> know an script to get rid of them? (I can use R, but very bluntly)

If you use rma() in the affy package, you will be doing essentially the 
same thing as gcrma() but without the step that uses the MM probes to 
estimate background. Also note that gcrma() doesn't use the MM probes in 
a naive way like Affy's MAS4 or MAS5, but estimates the true background 
after accounting for the 'stickiness' of the probe, based on the GC content.

Best,

Jim



>  
> Cheers
> marta 
>  
>  
> Marta Agudo PhD
> Departamento de Oftalmología
> Facultad de Medicina
> Campus Espinardo
> 30100 Murcia- Spain
> Phone:+34 968363996
>  
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623