User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk920
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920
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Location:
Switzerland
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2 days, 8 hours ago
Joined:
9 years, 8 months ago
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Posts by Axel Klenk

<prev • 124 results • page 2 of 13 • next >
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Comment: C: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... > results(dds, lfcThreshold = log2(1.5), alpha = 0.1) does not do what you apparently think it does, see ?results . You probably want something like > write.csv(as.data.frame(res[res$padj < 0.1 & res$log2FoldChange > log2(1.5),]), file="DEGs.csv") ...
written 10 weeks ago by Axel Klenk920
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Comment: C: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... Yes, if I read the figure legend and paper correctly, they did this as a first step to select candidates that were then tested in additional experiments, and the thresholds were apparently chosen to yield a manageable number of candidates. Why not. So, let me clarify, that I would not recommend usin ...
written 10 weeks ago by Axel Klenk920
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Answer: A: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... 1) Yes, in which case the resulting list of "DEGs" is expected to contain 10% false discoveries instead of 5%. 2) Sure, but you may want to check that the lfc of your "DEGs" is biologically meaningful in the context of your experiment and not "only" statistically significant. 3) I would not recomm ...
written 10 weeks ago by Axel Klenk920
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Answer: A: Microarray data analysis
... Dear Paul, that's a bit too concise.  I'm not really sure what you mean by "series matrix file"... If this is about a GEO series, use GEOquery::getGEO() to download it as an ExpressionSet, then use exprs(), pData(), fData(), etc. from the Biobase package to access the contents. ?pData Hope this ...
written 12 weeks ago by Axel Klenk920
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Comment: C: Cannot read Biom file
... Ouch, apologies for providing misleading help by posting a quick reply when I was about to leave my office... I had completely overlooked your paste() call... In your call to paste(), you're explicitly asking for no (empty) separator between file path and filename by setting argument sep = "". It w ...
written 12 weeks ago by Axel Klenk920
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Comment: C: Cannot read Biom file
... Dear voteroj, without looking at the read_biom() code, I guess it is trying to tell you that there is a problem with your filename.  These look like Windows paths and I'd suggest to simply add a colon to the drive letter, as in jsonbiomfile = "C:/Users/metagenomic/Desktop/otu_table_json.biom" (u ...
written 12 weeks ago by Axel Klenk920
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Answer: A: want the piece of the matrix I wanted
... Dear yueli7, try P[1:4, 5:7] or P[1:4, 5:ncol(P)] is that what you want? If yes, it is very basic R subsetting and not related to Bioconductor. It should be asked on StackOverflow or r-help and you may benefit from reading some introduction to R. Hope this helps. ...
written 12 weeks ago by Axel Klenk920
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Answer: A: could not find function "DESeqDataSetFromMatrix
... Dear Dastjerdi, as you don't show us the complete code you have used, I need to ask: have you loaded the package before use, e.g. library("DESeq2") ?library HTH. ...
written 12 weeks ago by Axel Klenk920
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Comment: C: Limma Voom produces many identical adjusted p-values
... Yep, that's why I usually use unadjusted p-values for plotting and ordering.  W.r.t. p-value vs. FDR, see ?p.adjust ...
written 8 months ago by Axel Klenk920
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Comment: C: Limma Voom produces many identical adjusted p-values
... Yes, they are fine, you can use them. Keep in mind that they are false discovery rates not p-values. ...
written 8 months ago by Axel Klenk920

Latest awards to Axel Klenk

Scholar 3 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Limma un moderated t-test
Scholar 15 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Centurion 15 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 2.5 years ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 2.5 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: basic R question: concatenate two numeric vectors grouped by element index

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