User: guidobarzaghi

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University of Copenhagen
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Posts by guidobarzaghi

<prev • 9 results • page 1 of 1 • next >
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Adjusting DESeq2 p-values through IHW using pathway information as covariate
... Greetings everyone, I have been reading about IHW as a method to adjust p-values for multiple testing by assigning weights to each hypothesis based on a prior (informative) knowledge. My rationale here is that given a list of differentially expressed genes (as returned by DESeq2, but also other met ...
deseq2 pathway ihw written 22 days ago by guidobarzaghi20 • updated 21 days ago by Michael Love22k
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Comment: C: DESeq2 w. pathway/network info as a prior knowledge
... Perfect! Thanks a lot for your help (again) ...
written 4 weeks ago by guidobarzaghi20
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Comment: C: DESeq2 w. pathway/network info as a prior knowledge
... Perfect! Thanks a lot for your help (again) ...
written 4 weeks ago by guidobarzaghi20
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Comment: C: DESeq2 w. pathway/network info as a prior knowledge
... As far as IHW is concerned, in my case the covariate used to compute the weights would be categorical (ideally a single number indicating with pathway is that gene involved in), wouldn't that be a problem? Otherwise, how else would you think of feeding that information to the model? ...
written 4 weeks ago by guidobarzaghi20
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Comment: C: DESeq2: paired samples + controls
... Alright, thanks a lot for you help! ...
written 5 weeks ago by guidobarzaghi20
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Comment: C: DESeq2: paired samples + controls
... Perfect, I think I got my head around this concept a bit more. My final doubt then is whether adding those two external controls would somehow mislead the analysis or would it just add no information. ...
written 5 weeks ago by guidobarzaghi20
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Comment: C: DESeq2: paired samples + controls
... Wow, that was quick (thanks a lot for that). I am only unsure about the meaning of "fixed effects", could you briefly elaborate on that? ...
written 5 weeks ago by guidobarzaghi20
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DESeq2 w. pathway/network info as a prior knowledge
... Good evening everyone, I was wondering if anyone has ever tried to perform a differential expression analysis using pathway/network information as prior knowledge. To be more specific, I am wondering if it is possible to feed DESeq2 the prior knowledge of pathways so that the algorithm is more pron ...
deseq2 pathway ihw written 5 weeks ago by guidobarzaghi20 • updated 4 weeks ago by Michael Love22k
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DESeq2: paired samples + controls
... Hi fellow DESeq'ers! I am trying to figure out how to model a DEA with *n* paired samples (so *n* conditions + *n* controls, where the two sample sets come from the same individuals) plus two unrelated controls. So overall I am dealing with *n* condition + *n*+2 controls. From the DESeq2 Vignette ...
deseq2 written 5 weeks ago by guidobarzaghi20 • updated 5 weeks ago by Michael Love22k

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