Hi
When I look at the FPKM files after cufflinks, if I ran a single comparison (control to experiment) and look at genes with a single transcript, then the FPKMs are identical in both files, as expected.
However, when I look at a cuffdiff run of Group 1: control 1 and control 2 (replicates) vs Group 2(experimental condition), and look at the same two files (gene and transcript FPKMs) at genes with a single transcript, then my Group 2 data (with only 1 replicate) still gives identical FPKMs, but my Group1 FPKMs are similar but not idnetical.
Is this a bug or something I dont understand in the algorithm?
Thanks
Noa
When I look at the FPKM files after cufflinks, if I ran a single comparison (control to experiment) and look at genes with a single transcript, then the FPKMs are identical in both files, as expected.
However, when I look at a cuffdiff run of Group 1: control 1 and control 2 (replicates) vs Group 2(experimental condition), and look at the same two files (gene and transcript FPKMs) at genes with a single transcript, then my Group 2 data (with only 1 replicate) still gives identical FPKMs, but my Group1 FPKMs are similar but not idnetical.
Is this a bug or something I dont understand in the algorithm?
Thanks
Noa