[BioC] is it a good idea not to consider low-intensity probesets in analysis?

[Weiwei Shi]

Dear gurus:

Sorry for this off-topic question.

I am thinking if it is a good idea to remove low-intensity probesets
of affymetrix.  For example, the following is a part of summary of
log2 intensity from the u133a probesets across 81 samples:

1007_s_at	1053_at	117_at	121_at
Min.   : 5.966	Min.   :4.635	Min.   :2.925	Min.   :2.466
1st Qu.: 8.194	1st Qu.:5.366	1st Qu.:3.381	1st Qu.:2.553
Median : 8.873	Median :5.570	Median :3.509	Median :2.604
Mean   : 8.824	Mean   :5.639	Mean   :3.816	Mean   :2.801
3rd Qu.: 9.522	3rd Qu.:5.898	3rd Qu.:3.919	3rd Qu.:2.860
Max.   :11.132	Max.   :7.094	Max.   :6.650	Max.   :3.828

My question is, does it make sense to remove the probeset 121_at for
its max(log2 intensity) is only 3.828?

thanks,

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III