User: j.bergenstrahle

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Posts by j.bergenstrahle

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Diffbind dba.report error
... Hi Rory, I see that I didn't have the latest release. I will use your workaround (works well) until the new release, thanks for the quick reply! Best, JB ...
written 3 months ago by j.bergenstrahle20
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Diffbind dba.report error
... Hi! I'm using DiffBind for ATAC-seq data, and everything runs smoothly except one thing -> I cant make a dba.report for one of my contrasts. All steps from loading -> counting -> analyzing seems to work, I get differently called peaks etc. I have 4 different conditions and 6 contrasts (out ...
diffbind written 3 months ago by j.bergenstrahle20
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Comment: C: Diffbind data extraction after DE analysis
... Ahh there I go, poorly searched on my side, thanks for the quick answer Gord! ...
written 3 months ago by j.bergenstrahle20
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Diffbind data extraction after DE analysis
... Hi, I'm currently using Diffbind for my ATAC-seq pipeline. After calling the dba.analyze function you can do various plots via e.g. dba.plotMA. But is there some simple way to extract the logFoldChange, pvalues etc from the DBA object? I guess this should be easy since the object obviously stores t ...
diffbind written 3 months ago by j.bergenstrahle20 • updated 3 months ago by Gord Brown500
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Comment: C: fdrtool - correction of p-values - course found on huber.embl.de
... Maybe I should "mark" this question as completed? (Not sure the appropriate approach when posting something like this?)  ...
written 4 months ago by j.bergenstrahle20
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fdrtool - correction of p-values - course found on huber.embl.de
... Hello, I originally emailed this question to c Klaus at EMBL and got a really good and well written response. I promised that I should post the question and answer here since more people might find it interesting, especially the approach one might take to explore your data if p-value distributions ...
p-value distribution fdrtool written 4 months ago by j.bergenstrahle20

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