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-   -   how does cuffdiff calculate replicate FPKM values? (

KateShepard 05-19-2016 02:18 AM

how does cuffdiff calculate replicate FPKM values?

I have two conditions, 5 replicates for each. After running cuffdiff I noticed the FPKM values in gene_exp.diff for one condition do not make sense.

For example, the 5 replicate FPKM values for geneA in one condition are

109.763 79.6751 109.132 53.3997 123.322.

When I look at the FPKM values for that gene in gene_exp.diff or genes.fpkm_tracking files (output of cuffdiff) I get an FPKM value of 288.685 (conf_lo 109.888, conf_hi 467.481).

My question is how does cuffdiff calculate the condition FPKM value based on the biological replicates? The explanation on the cufflinks website does not make it clear to me.

Thank you for your help,

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