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Old 12-21-2012, 11:17 AM   #1
Germwise
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Location: Ohio

Join Date: Sep 2011
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Default Newbie needs help with DGElist for EdgeR analysis

Please excuse my ignorance if this information is available somewhere. Perhaps I do not know the correct terms to use for the search...

I have a RNA seq time series with 8 time points, 2 treatments (mock and treatment) and 2 replicates such that we have 32 total counts files.

I've been reading through different guides but I find either multiple replicates or time series, or treatments but not all.

How do I organize my files and the design for EdgeR analysis? If someone could point me to a tutorial that explains the syntax that would also help me arrive at the answer.

I think the issue I am having is I find multiple examples but do not understand the reasoning for differenes in syntax.

Thank you all in advance!
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Old 12-31-2012, 04:41 AM   #2
Germwise
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Post holiday bump. Can anyone point me in the right direction?
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Old 01-01-2013, 02:46 PM   #3
Gordon Smyth
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See the edgeR User's Guide (making sure you have the latest version), especially Chapter 3.

If the examples and case studies are not enough, then see Section 1.3 "How to get help".
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