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Ken Termiso
▴
250
@ken-termiso-1087
Last seen 10.3 years ago
Hi all,
>From a recent experiment with affy 133v2 chips, I had four different
cases,
each with three controls and three experimental chips. The four cases
are
analyzed separately, since they all rec'd different treatments.
Combining
them doesn't work since they are all so different.
Due to the world being an imperfect place, I only have technical
replicates,
so all of my statistics are based on these technical replicates. (In
the
past, from similar experiments, I've been able to confirm ~90% of
differential expression with RT-PCR based on this strategy).
The problem is, that for one of the cases, two of the experimental
chips are
much, much brighter than the other one. The six chips were normalized
together using RMA, which for this tissue has been the superior
normalization all along vs the others we've tried (GCRMA, MAS5.0, and
li-wong). Here is a random selection of probesets to illustrate what
I'm
saying -
Control 1 Control 2 Control 3 Exp 1
Exp 2 Exp 3
3514.66 2917.78 1960.94 3915.28
13710.44 13385.72
2272.28 2004.44 1387.7 2751.73 8759.5
8596.44
568.71 396.12 335.61 614.27
1617.23 2374.7
1754.51 1250.99 1082.94 1781.94
7261.92 7679.01
2156.23 1709.61 1394.24 2793.15
8053.99 11112.1
468.04 452.48 382.7 605.1
1692.47 3202.71
Our (somewhat lousy) core processed these chips about a year ago, so
I'm
wondering if there's anything I can do to deal with the last two
experimental chips, which are way, way off...I'd like to bring them
down to
the realm of the other exp chip without introducing any bias before
doing
stats to find significant, diff expressed genes.
Thanks in advance,
Ken