User: krassowski.michal

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Posts by krassowski.michal

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Comment: C: A part of the DESeq2 documentation may be misleading on the steps needed to chan
... I found it, it was my fault. This is the actual code and the error is in question - I did not save the result from nbinomWaldTest(dds) onto new dds. Edit, because I cannot post more comments due to new-users restrictions: Thank you for maintaining DESeq2 and for your help here. ...
written 12 weeks ago by krassowski.michal0
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Comment: C: A part of the DESeq2 documentation may be misleading on the steps needed to chan
... It's not a big problem really - I posted here because I needed 1.5 hours to find out why it's not working as I thought it would - of course, an experienced user should not have that problem, but I thought that maybe this will help someone, someday. ...
written 12 weeks ago by krassowski.michal0
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Comment: C: A part of the DESeq2 documentation may be misleading on the steps needed to chan
... I think that you may have missed my point. Please have a look at the last example - it produces an error if I follow the first quote literally. Re-using characters - this is just a quick minimal reproducible example, I missed the quotes ;) ...
written 12 weeks ago by krassowski.michal0
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Comment: C: A part of the DESeq2 documentation may be misleading on the steps needed to chan
... I think that my confusion arose from the re-use of dds which is used to mean "DESeqDataSetFromMatrix" in one place and "DESeq" in the other. Thinking like a C-programmer I've overwritten the first with the second one. But it might be an issue with the vignette as well. ...
written 12 weeks ago by krassowski.michal0
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Steps needed to change design (relevel factors) in DESeq2
... The vignette states that: > Instead, one need only run `nbinomWaldTest` to re-estimate MLE > coefficients – these are necessary for `apeglm` – and then run `lfcShrink` > specifying the coefficient of interest in `resultsNames(dds)`. > > We give some examples below of producing equiv ...
deseq2 written 12 weeks ago by krassowski.michal0
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Comment: C: Limma linear fit residual standard deviation calculation
... Thank you for taking the time to answer this question, I really appreciate it. I find the second reference very useful. Thank you! ...
written 3 months ago by krassowski.michal0
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Limma linear fit residual standard deviation calculation
... This is a low-level question, but I am very curious about the reason for limma calculating the residual standard deviation (`sigma`) in `lmFit` (or more precisely, `lm.series`) as: ``` # 1. lm.series sqrt(mean(out$effects[-(1:out$rank)]^2)) ``` rather than: ``` # 2. what I would expect x <- out ...
limma written 3 months ago by krassowski.michal0 • updated 3 months ago by Gordon Smyth39k
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Answer: A: PLAGE method fails in GSVA if an overlap between gene sets and genes in expressi
... I hypothesized that the gene sets with overlap of one are the issue; I tried another such one - for entrez ids limited to 1000 one of such gene sets is KEGG_GALACTOSE_METABOLISM and the problem appeared again. Then I filtered out all gene sets with overlap lower than two and tried to run my program ...
written 9 months ago by krassowski.michal0
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
... I've been using GSVA with three methods: gsva, ssgsea and z-score for some time now, with success and without problems. However, when I tried to use the forth method - PLAGE - I found out that it does not work with some of the gene sets. Specifically I've discovered that using MSigDB Kegg collection ...

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Scholar 9 months ago, created an answer that has been accepted. For A: PLAGE method fails in GSVA if an overlap between gene sets and genes in expressi

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