Hi all,
I use cuffdiff to compare my RNA-Seq samples, and the result I got is inconsistent.
For example, I have three samples, S1, S2, and S3. I ran cuffdiff for a pair first S1 vs. S2. Then, I ran cuffdiff for all three samples. Since cuffdiff does pair-wise, it reports all pairs. S1 vs. S2; S1 vs. S3; and S2 vs. S3.
The results I got for S1 vs. S2 from these two runs are different. I assume they should be the same. I'm wondering is there anything I did wrong? or cuffdiff considers more factors when sample is more?
Thanks,
Xiaoyu
I use cuffdiff to compare my RNA-Seq samples, and the result I got is inconsistent.
For example, I have three samples, S1, S2, and S3. I ran cuffdiff for a pair first S1 vs. S2. Then, I ran cuffdiff for all three samples. Since cuffdiff does pair-wise, it reports all pairs. S1 vs. S2; S1 vs. S3; and S2 vs. S3.
The results I got for S1 vs. S2 from these two runs are different. I assume they should be the same. I'm wondering is there anything I did wrong? or cuffdiff considers more factors when sample is more?
Thanks,
Xiaoyu
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