[BioC] three group ANOVA

kfbargad@ehu.es kfbargad at ehu.es
Fri Dec 2 16:09:13 CET 2005

Dear List

I am trying to find out if the mean expression values of Q-PCR differ 
for a group of 192 genes in three different sample groups. I am mainly 
interested in the F value, not any particular contrasts. I have 
created an exprSet out of my QPCR 
data using the following


Expression Set (exprSet) with 
        192 genes
        40 samples
                 phenoData object with 1 variables and 40 cases
                cov1: read from file

How can I proceed now? I thought of using linear models and then 
obtain the F value from fit3$F.p.value for the fit, but I got the 
following errors:

>treatments = factor(c
0,0,0,0,0),labels = c("N0","N1","N2"))
>design = model.matrix(~0+treatments)
>fit <- lmFit(exprs(myEset),design)
>contrast.matrix = makeContrasts(N1-N0,levels = design)
>fit2 = contrasts.fit(fit,contrast.matrix)
>fit3 = eBayes(fit2)
Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = 
stdev.coef.lim) : 
        No residual degrees of freedom in linear model fits



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