User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk920
Reputation:
920
Status:
Trusted
Location:
Switzerland
Last seen:
26 minutes ago
Joined:
9 years, 6 months ago
Email:
a*********@idorsia.com

Posts by Axel Klenk

<prev • 121 results • page 2 of 13 • next >
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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 17 days 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 19 days 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 19 days 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 20 days 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 20 days 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 6 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 6 months ago by Axel Klenk920
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Answer: A: Limma Voom produces many identical adjusted p-values
... Dear b.nota, yes, it is a known effect of the BH p-value adjustment, not limma or voom. Cheers,  - axel   ...
written 6 months ago by Axel Klenk920
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Answer: A: R packages for differential expression analysis of raw data from arraystar micro
... Dear Nick, I have never used nor even heard of arraystar microarrays, but in general the limma package provides all the functionality for importing, preprocessing and analyzing microarray data. It comes with an extensive user's guide which may help you to get your data analyzed. Good luck,  - a ...
written 7 months ago by Axel Klenk920
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Answer: A: No differential expression with limmaCtData possible
... Dear h.roest, looking at your code, I see that gnorm.raw.cat.Filt being used without ever being read from a data file or otherwise created.  Is it possible that you're running your R script line by line and accidentally skipped one or more lines?  Just a guess. Cheers,  - axel   ...
written 7 months ago by Axel Klenk920

Latest awards to Axel Klenk

Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Limma un moderated t-test
Centurion 12 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Scholar 12 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 2.3 years ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 2.4 years ago, voted at least 25 times.
Teacher 3.5 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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