Question: Retrieve gene sets from Cuffdiff/Cuffnorm output with self defined criteria
gravatar for Wet&DryImmunology
3.8 years ago by
Wet&DryImmunology220 wrote:



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. 







rna-seq cuffdiff cufflinks R • 1.2k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Wet&DryImmunology220
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