User: Jonas B.

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Jonas B.0
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Posts by Jonas B.

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Comment: C: DESeq2 normalization vs VST vs rlog
... Dear Micheal, Thank you for your time and answers. It's all clear now. Kind regards, Jonas ...
written 12 weeks ago by Jonas B.0
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Comment: C: DESeq2 normalization vs VST vs rlog
... Indeed, I am sorry, it is used in code where 20 genes get preselected, on which later on the normTransform function (log2(n+1)) was performed. I should have looked more carefully. Do you mind still sharing the answer to my previous question concerning the function "counts(dds, normalized=TRUE)"? ...
written 12 weeks ago by Jonas B.0
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Comment: C: DESeq2 normalization vs VST vs rlog
... Dear Michael, thank you for your quick reply. I've read the vignette and in the future I will definitely go for VST then. About the normalized counts I've obtained using the function "counts(dds, normalized=TRUE)": - The normalized counts obtained here, are they also log2 transformed? I was una ...
written 12 weeks ago by Jonas B.0
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Comment: C: DESeq2 normalization vs VST vs rlog
... It came to mind that the function: counts(dds, normalized=TRUE), might already return log2 transformed data? (However, this is not described in: https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/counts) ...
written 12 weeks ago by Jonas B.0
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Comment: C: DESeq2 normalization vs VST vs rlog
... As a side note: I did find a recent question addressing normalization ( https://support.bioconductor.org/p/123651/ ) , however it leaves my question unanswered on whether or not I could also use the counts function ( *I guess it's wrong, but I am not sure. Maybe it is still usable...* ) and which o ...
written 12 weeks ago by Jonas B.0
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DESeq2 normalization vs VST vs rlog
... Hi all, after consulting the manual on data normalization, I have one question left to ask: The way I see it, there are 4 ways described to obtain normalized data: - The first one is to extract data, normalized using the normalization factors for a gene x sample matrix, and size factors for a si ...
deseq2 written 12 weeks ago by Jonas B.0 • updated 12 weeks ago by Michael Love26k
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Comment: C: Question concerning the testing of interactions using the group design and the u
... Dear Micheal, Thanks a lot! Using betaPrior works just fine for me! Kind regards and happy Easter, Jonas ...
written 19 months ago by Jonas B.0
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Question concerning the testing of interactions using the group design and the use of lfcShrink() (DESeq2)
... Hi all,   My question concerns testing interactions using the group design and the use of lfcShrink():   As a short intro, my experimental design: - three treatments: control, mild, severe - three developmental zones: mer, elo, mat   Before lfcShrink() was introduced, the resultsNames() funct ...
deseq2 written 19 months ago by Jonas B.0 • updated 19 months ago by Michael Love26k
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Thanks a lot, Michael! ...
written 21 months ago by Jonas B.0
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Thank you Michael! You wrote: "...so you can compare two arbitrary levels of a factor variable." This looks like you referred to a one factor design. So in a two factor design, this means that I can compare any combination the two factors against each other using the group functionality, right? ...
written 21 months ago by Jonas B.0

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Popular Question 13 months ago, created a question with more than 1,000 views. For Are two biological replicates enough for a transcriptome analysis using DESeq2?

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