[BioC] paired t-test
James W. MacDonald
jmacdon at med.umich.edu
Wed May 13 15:18:32 CEST 2009
Yogi Sundaravadanam wrote:
> Hi all,
> I have six samples with the following design
> ID Sample Type C1 A Control C2 A Treated
> C3 B Control C4 B Treated
> C5 C Control
> C6 C Treated
> A, B, and C are three patients
> Would a paired t-test work better than one-way ANOVA here? Do I need
> more replicates?
You definitely want to account for the intra-patient dependence
structure somehow. One way would be to do a paired t-test. The other way
would be to do a linear mixed model-ish thing using
duplicateCorrelation() to capture the intra-patient correlation.
There have been numerous posts about the latter, and if I am not
mistaken there is an example in the Limma User's Guide as well.
> thanks for your help
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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