Question: Sample order in Deseq2?
gravatar for vebaev
11 months ago by
vebaev130 wrote:

Hi, are the right order in Deseq2 is first "treated" and second "control" to produce changed expression in the treated sample?


ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by vebaev130
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Using Treated as the first factor is most likely what you want to do. The example under "What it does > Inputs" of the lower help section for the tool has an example that addresses your use-case.

As with most tools, options are explained on the tool form (abbreviated) and these match up with the underlying wrapped tool's linked manual help (and often publication). Many tools also have a google group/support resource and are frequently discussed by the larger Bioinformatics community at Scientific advice would be applicable whether using the tool in Galaxy or not.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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