Hi,all

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
treatment.
How can I solve this problem? Is it right only using RMA value for limma and
igore present/absent calls?


Regards!


haiyan

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