Thanks for quick reply.
Where can I see which version are being used? It does not say in the attached
(in my first e-mail) info-view after the run.. What does Cuffdiff (version
0.0.5) mean then? What version was it before? It is a great difference in
number of DE genes..
I mostly meant it was the same now in August with more DE genes for all
different type of analysis that I have previously done (consistent new results
with no settings changed), I really do not see more DE genes when 5 vs 6
samples compared to 1 vs 2 samples. But that might be due to more biological
I look forward to the update, will that mean another version of Cuffdiff again?
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, August 22, 2013 8:04 PM
To: Johanna Sandgren
Subject: Re: [galaxy-user] Cuffdiff changes
I am wondering why Cuffdiff suddenly gives many more significant DE genes?
Cuffdiff was recently updated to version 2.1.0; this update likely explains the
different results that you see.
I have rerun several analysis, also with more samples in each group, all give
much more significant genes. Why?
More samples = more power to accurately estimate expression levels = more DE
Also, will replicate information soon be included in output files?
Replicate data will be available when we next update our server. This should
occur in about 3 weeks.
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