Question: Sample order in Deseq2?
0
gravatar for vebaev
28 days ago by
vebaev130
Bulgaria
vebaev130 wrote:

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

Thanks!

ADD COMMENTlink modified 28 days ago by Jennifer Hillman Jackson23k • written 28 days ago by vebaev130
2
gravatar for Jennifer Hillman Jackson
28 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

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 https://www.biostars.org/. Scientific advice would be applicable whether using the tool in Galaxy or not.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 28 days ago by Jennifer Hillman Jackson23k
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