[BioC] Limma contrasts

[Xinxia Peng]

Hi All,

I want to know if there is a difference between any two samples out of 7
in this situation:

I am doing single channel analysis of two color arrays using Limma. The
dataset has 7 different samples and each sample has different number of
biological replicates (2 to 4). I included an coefficient for each
biological replicates in the linear model, considering each biological
replicate has different number of technical replicates. The 'Technical
Replication' section in Limma's user guide shows an example of making
contrast matrix for comparisons of interest. How do I construct a
contrast matrix to test if their means are same? Or I need do ANOVA
analysis of those fitted coefficients?

Thanks,
Xinxia