I have two datasets of Microarray from the Affymetrix platform, and I have normalized them using gcrma package.
One dataset has 27 samples and another has 66 samples, and I want to identify the differentially expressed genes between two dataset by running the wilcox.test in R, because I have not any idea about the distribution of gene expressions I can not use the t.test. After running wilcox.test, the p-values for most of the genes are less than 0.001!
How can I identify genes with the significant differential expression between these datasets?
Thanks in advance.