[BioC] Selection of quantitative differences b/w two M vs A plots
after rma
Anthony Bosco
anthonyb at ichr.uwa.edu.au
Thu Mar 4 01:38:13 MET 2004
Hi.
In my experiments I have control and stimulated cell cultures for
individuals with and without disease (usually no replicates, but
sometimes up to 3 replicates).
Therefore I have two M vs A plots, control verses stimulus for the
disease group, and control verses stimulus for the group with no
disease.
For each group, I analyse Affy data with rma and generate M vs A plots.
I define everything with M value > 0.45 (in a 2 chip comparison) as
differentially expressed, but some genes are differentially expressed
in the disease and no disease groups, but at a much higher level in
one of the groups.
Currently since I define the noise as m = 0.45, I just simply
subtract the m values for any gene which is differentially expressed
in both M vs A plots, and if the difference is greater than 0.45 I
call that different between both groups.
1) Is this correct?
2) Does any one know how many false positives to expect in two chip
comparisons with Affy chips
Regards
Anthony
--
______________________________________________
Anthony Bosco - Cell Biology Research Assistant
Institute for Child Health Research
(Company Limited by Guarantee ACN 009 278 755)
Subiaco, Western Australia, 6008
Ph 61 8 9489 , Fax 61 8 9489 7700
email anthonyb at ichr.uwa.edu.au
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