Hi,I am trying to analyze output of Cufflinks pipelines.
I can use CummeRbund to visuallize the "differentially expressed" gene sets defined by the Cufflinks program.
> gene_diff_data <- diffData(genes(cuff),"Sampe1”,”Sample2”)
> sig_gene_data <-subset(gene_diff_data,(significant =="yes"))
> csHeatmap(myGenes,clustering = 'both')
But the definition of "differentially expression" in the Cufflinks(Cuffdiff) is quite stringent, as far as I have understood,
that might leave out a lot of "seemly not differentially expressed" genes.
Is there any way to retrieve gene sets with some self defined criteria, something like " fold change > 2 " between two samples , "fpkm >10" for all the samples. I guess this might be very easy for people with sophistigated coding skills, but is there any solution for someone who are not professional bioinformatists, say a R package?
Thanks for any kind suggestion.