I don't know if anyone else has experienced a similar problem as I had. I am analyzing several RNAseq samples following the tophat-->cuffdiff pipeline to determine differentially expressed genes. I started the analysis two weeks ago and got some preliminary results on my treatment vs control comparison (6 samples in total, 3 vs 3) using cufflinks 1.1.3. The cuffdiff program indicated that there are about 173 genes differentially expressed between two conditions (from the gene-exp.diff file).
When cufflinks released the newest version 1.2.0 on Nov. 23th, I reran the algorithm and saw a HUGE difference on the cuffdiff results using EXACTLY the same command and the same human reference annotation file hg19. This time, the cuffdiff indicated a total of 5359 differentially expressed genes (from the gene-exp.diff file).
I am totally confused and do not know which version I should trust. How come there is such a big difference on the differentially expressed genes?
Did anyone experience a similar problem?
When cufflinks released the newest version 1.2.0 on Nov. 23th, I reran the algorithm and saw a HUGE difference on the cuffdiff results using EXACTLY the same command and the same human reference annotation file hg19. This time, the cuffdiff indicated a total of 5359 differentially expressed genes (from the gene-exp.diff file).
I am totally confused and do not know which version I should trust. How come there is such a big difference on the differentially expressed genes?
Did anyone experience a similar problem?
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