[BioC] RMA normalization and MAS5.0 detection calls

Naomi Altman naomi at stat.psu.edu
Thu Dec 7 16:19:40 CET 2006

If the probeset is mainly absent in 1 condition and mainly present in 
another, then I think you would not want to filter these out, since 
this seems to be an important gene for understanding the difference 
in conditions.


At 08:25 AM 12/7/2006, haiyan wu wrote:
>I'm using Bioconductor for analyze some Affymetrix Genechip.When I use RMA
>to normalize probe sets,it give no info for whether the probe sets present
>or absent.
>So I  get these  info from MAS5 detection calls.But in some case,the DE
>probes sets which was selected seems absent .On other situation for contrast
>different treatment,
>some probe sets presnt in treatment1 and absent in treatment2, but limma
>give me a conclusion that this probe sets have no changed between these 2
>How can I solve this problem? Is it right only using RMA value for limma and
>igore present/absent calls?
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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