[BioC] Affy: Present calls in an eset

[Phguardiol at aol.com]

Hi,
my understading ot the A/P calls from Affy MAS5 is that they represent a way 
to "evaluate" the background signal. 
In that way you could have a high background, ie, a high MisM signal, and 
despite the PM signal is identical, for instance 500, the this gene is going to 
be considered as Absent, which could be that your gene is not expressed, but 
could also be due to the design of the probe set rather than to the fact that 
the gene is not expressed....

Detecting if a gene is expressed or not with Affy chips is for me almost 
another question, a difficult one ! my threshold is 70 (2^RMA value) but it is 
likely that at this value some genes are expressed it is hust that below tis 
value I consider, arbitrarly, that it is difficult to validate something because 
of the noise.
Anybody can correct me if I m wrong with all this since I  still new in ths 
field as well !
Hope it helps
Philippe  

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