[BioC] Affy: Present calls in an eset
Phguardiol at aol.com
Phguardiol at aol.com
Wed Oct 8 11:29:09 MEST 2003
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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