What is the "value" in output of Cuffdiff

[bela]

Hi,

I am wondering what does the "Value" mean in the gene_exp.diff when there are multiple samples in one condition? I've run Cuffdiff with each single sample and found that it is not the mean of the FPKM value for each sample. So I am wondering how it is calculated? Thanks.

BZ

[bela]

Could anyone answer my question? I am new to RNAseq, so the question might sound naive. But I really want to know it and can't find the answer myself. Thanks.

BZ

[fuad193]

It is FPKM, but it is different than cufflinks FPKM becuase of the difference in the default options passed to each.

[mastal]

What is the "value" in output of Cuffdiff

The Cuffdiff gene_exp.diff files report gene differential FPKMs.

Cuffdiff tests differences in the summed FPKM of transcripts sharing each gene_id.