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 reasons.

I look forward to the update, will that mean another version of Cuffdiff again?

Kind regards,

Johanna

From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Thursday, August 22, 2013 8:04 PM
To: Johanna Sandgren
Cc: galaxy-user@lists.bx.psu.edu
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 genes.

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.

Best,