I am fairly new to microarray analysis. I have 40 arrays from four phenotypes and would like to compare the gene expression among the four subtypes.
For this i used bead array (since the arrays are illumina based), preprocessed with BASH/HULK and summarised it and ran neqc for background correction and normalisation and finally have log2 expression data as an ExpressionSetillumina.
I then use this for carrying out differential expression analysis using Limma. I would like to compare the gene expression of one subtype with the others. For this I first use the design matrix and define the arrays corresponding to a subtype with one and the rest 0. I then compare the groups. Note that there are different number of repilcates in each subgroup.
Sadly I donot get any differential expression which is very unlikely and I am sure there is something wrong.