I have been handed a list of genes from an RNAseq experiment and I have no information about how it was generated as it was done a while ago by a company. I have the lis of genes in columns and pvalues/fold change for different comparisons. I also have the normalised expression values for each gene from each donor.
I have been asked to do some pathway analysis on this and was wondering about the best way to carry this out? I would rather not use arbitrary cut-offs of p-values etc but would rather do some kind of GSEA in R.
It seems the limma package integrates analyses like camera for this, but am not sure I can simple use the data I have or which format they need to be to use within the limma package?
Any other advice about which packages to use?