DESEQ2 Differential Expression controlling for two factors
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Bine • 0
@bine-23912
Last seen 8 days ago

Dear all,

I have used DESeq2 for my Differential Expression Analysis and with

~batch + gender

I controlled for the different batches.

Now I would like to control not only for gender instead also for another variable. Can I control for 2 different variables in the model? Or do I manually need to remove it before through maybe "remove batch effect" functions?

Thank you for any hint!!

DESeq2 • 123 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

The answers to your questions are

  1. Of course
  2. No, that's not how it works

But I suspect you have a more directed question. If it's 'how should I analyze my data', you might get lucky and get an answer, but probably not, because that's not really what this site is for. If it's 'I did this and it did not work and here is the error message', then by all means post that.

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Alternatively, for questions that are not purely technical and therefore do not require the developer's "how-it-works-under-the-hood"-expertise you can post at biostars.org, it is a general community for everything related to bioinformatics. If you do please add the necessary details (this goes for any community). In your case that would be a table listing which samples belongs to which group(s) to see whether covariates (=variables) can be meaningfully modelled or are nested with each other.

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