User: Alan

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Alan0
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Canada
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Posts by Alan

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Comment: C: To analyze the overall variance, which one to choose, vst or DESeq2 normalized c
... OK I see, thank you, Michael. ...
written 12 weeks ago by Alan0
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Comment: A: To analyze the overall variance, which one to choose, vst or DESeq2 normalized c
... Hi Michael, May I ask: 1) Could you specify a little bit more about what are the some of reasons for favoring VST over rlog? 2) To clarify, the VST procedure is just for purpose of clustering and visualization, right? It (the counts after VST) basically is not involved in testing for pairwise DE ...
written 12 weeks ago by Alan0
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Comment: C: How to set up the Wald test testing for log2 fold change above a threshold, and
... Thank you very much, Michael! I am very sorry for making you write again. I used another computer at first, and so I posted again. Thank you for your patience and explanation!   -Alan ...
written 3 months ago by Alan0
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Comment: C: How to set up the Wald test testing for log2 fold change above a threshold, and
... Hi Michael, Thank you very much indeed! A few follow up questions on this same LFC shrinkage issue: (I decide to go with apeglm after some reading) #1. Just to clarify: again, take the pasilla dataset as an example, if I wanna use the apeglm method to shrink LFC, and I am interested only in genes t ...
written 3 months ago by Alan0
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How to set up the Wald test testing for log2 fold change above a threshold, and interpret the result correctly?
... Hi Michael and community, My question this time is about how to set up the Wald test log2 fold change above a threshold, and how to interpret the result correctly. #1. Take the pasilla dataset (in the DESeq2 vignette) as an example, if I am interested only in genes that show |log2 FC| >2, and I ...
deseq2 written 3 months ago by Alan0 • updated 3 months ago by Michael Love17k
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Comment: C: Is it reasonable to run DESeq2 on only a subset of transcripts of the original r
... OK, I see. Thank you very much for explanation, Michael.  Alan ...
written 3 months ago by Alan0
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Comment: C: Is it reasonable to run DESeq2 on only a subset of transcripts of the original r
... Hi Michael, Thank you for your quick reply. I understand it's essential to to give DESeq2 enough info (genes) to allow more accurate estimation of size factors and dispersion.   Can I sort of push my question one step further: for instance, in my experiment, I am most interested in comparing the ...
written 3 months ago by Alan0
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Is it reasonable to run DESeq2 on only a subset of transcripts of the original raw count matrix?
... Hi Michael and community, As always, thank you for your devotion in DESeq2. I'd like to ask about: is it reasonable to to run DESeq2 analysis on only a "subset" of the original raw count matrix? (would the DESeq2 statistical model still apply?) For instance, if I am only interested in the coding ge ...
deseq2 written 3 months ago by Alan0 • updated 3 months ago by Michael Love17k
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Comment: C: DESeq2 plotCounts() function-what is the unit on y axis?
... Thank you for your very prompt reply and explanation, Michael!   Alan ...
written 3 months ago by Alan0
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DESeq2 plotCounts() function-what is the unit on y axis?
... Hi Michael and community, Thanks for the work and efforts on DESeq2! I've had this question for some time, I went through quite a number of posts, the manual, and the vignette, but can't really find the answer. What is the unit of the "normalized count" of the y axis of the "plotCounts" plot? plo ...
deseq2 written 3 months ago by Alan0 • updated 3 months ago by Michael Love17k

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