[BioC] MAS5 present/absent calls
eblanc at ebi.ac.uk
Mon Mar 6 11:39:55 CET 2006
The MAS5 original documentation
describes how the Present/Absent calls are computed. This document
emphasizes that the cutoff values (alpha1=0.04 and alpha2=0.06) for
attributing a P/M/A call given a P value are suitable for probesets
which have between 16 and 20 probes. The man page for mas5calls states
that the bioconductor implementation in the affy package uses the same
values. I have 2 questions about that:
1) What are the guidelines when the number of probes per probeset is
lower (11 to 14) ?
2) Does anybody knows what is the default MAS5 behaviour when the number
of probes per probeset is lower ?
Thanks for your help,
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