Q:Accessing Functional data with CummeRbund from Cufflinks

[Saint-Louis]

Hello,

I would like to evaluate KOG_class differences with CummeRbund in the cufflinks output. A file gene_exp_func.diff was created that shows the KOG_class etc when opened in EXCEL. Maybe, my R and CummeRbund skills are too poor to work this out myself. Could anyone help assessing the properties of my transcriptome comparison on the functional.

A more general question. Is there a manual or manuscript explaining how to conduct an assessment of transcriptome difference and find the transcripts/genes of interest?

Thanks