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.

For example:

> gene_diff_data <- diffData(genes(cuff),"Sampe1","Sample2")
> sig_gene_data <-subset(gene_diff_data,(significant =="yes"))
> geneids<-c(sig_gene_data$gene_id)

> myGenes<-getGenes(cuff,geneids)

> 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.