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Old 06-22-2018, 05:55 AM   #1
Damien P.
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Location: Strasbourg

Join Date: Jun 2018
Posts: 1
Default JunctionSeq, batch effect

Hello,

I am using JunctionSeq and I have a question about batch effect. In my data, I have a batch effect, separating the samples belonging to the same condition in two groups. I read the documentation but I am not sure how to take into account batch effect.
I thought to add, in the runJunctionSeqAnalyses function, a dataframe containing only one column in use.covars argument, which corresponds to the batch effect, and then to change test.formula0: formula(~batch+sample+countbin) and test.formula1: formula(~batch+sample+countbin+condition:countbin).
Do you think it is the good way to take into account a batch effect?

Thank you very much!
Damien
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