[BioC] RMA t-test

[James MacDonald]

I would be cautious about using RMA with only two chips. You will be
estimating the probe-specific intensity with only two observations, so
it is doubtful that the estimate will be very accurate. I recall reading
somewhere that a good minimum number of chips is around 5-6 for RMA.

As for a t-test with only one observation per group, this is not
possible. How are you going to estimate the variance for each group?
Without replication all you can do is ratios, and you are then stuck
with the assumption that large ratios equal significant differences.

Jim




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> DMITRY GRIGORYEV <dgrigor1 at jhmi.edu> 07/28/03 12:08PM >>>
Hi everyone.

One quick question.
When I run RMA on just two chips, how could I conduct pairwise t-test
for each probe set between these chips?

Thank you 

Dima

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