[BioC] help with lumi and limma

[Taylor, Katie]

Hello,

I hope that someone can help me. I have done an experiment using Illumina DASL WG array. I have 48 samples split into 6 groups. I have normalised them all together using lumi; vst followed by quantile normalisation. I have then gone on to use limma to get the topTables for each of the comparisons that I make. The script works well and produces everything that I wanted. However I have a problem with the topTables. When one group(NC) is compared to the others, every gene is shown to be significant. However, when the other groups are compared together they are more sensible with some genes showing differential expression and others not. Has anyone come across this problem before or know what I need to do? 

Thanks,

Katie