[BioC] limma design, 3 biological reps (two with a tech rep, one without)
Ryan Basom
rbasom at fhcrc.org
Mon May 11 23:26:31 CEST 2009
Hi,
I'm trying to use limma to analyze the following: Originally, there
were 6 arrays (3 biological reps, each with a dye-swap hybridization).
There was a technical issue with one of the arrays, leaving me with an
'unbalanced' design:
SlideNumber Name FileName Cy3 Cy5
1 PI-1_vs_DMSO-1 PI-1_vs_DMSO-1.txt PI DMSO
2 DMSO-2_vs_PI-2 DMSO-2_vs_PI-2.txt DMSO PI
3 PI-2_vs_DMSO-2 PI-2_vs_DMSO-2.txt PI DMSO
4 DMSO-3_vs_PI-3 DMSO-3_vs_PI-3.txt DMSO PI
5 PI-3_vs_DMSO-3 PI-3_vs_DMSO-3.txt PI DMSO
I'd like to attempt to include the sample without a technical replicate
and would like to know if this this would be an acceptable way to handle
this situation? ('pool' is a MAList containing 5 the arrays listed in
the above order).
design <- cbind(PI1vsDMSO1 = c(-1, 0,0, 0,0), PI2vsDMSO2 = c(0, 1,-1,
0,0), PI3vsDMSO3 = c(0, 0,0, 1,-1))
cont.matrix<-makeContrasts(PIvsDMSO = (PI1vsDMSO1 + PI2vsDMSO2 +
PI3vsDMSO3)/3, levels=design)
fit<-lmFit(pool, design)
fit<-contrasts.fit(fit, cont.matrix)
fit<-eBayes(fit)
Thanks,
Ryan
--
Ryan Basom
Genomics Resource
Fred Hutchinson Cancer Research Center
Seattle, WA
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