User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk830
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830
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Location:
Switzerland
Last seen:
5 days, 7 hours ago
Joined:
9 years, 1 month ago
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Posts by Axel Klenk

<prev • 106 results • page 1 of 11 • next >
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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 5 weeks ago by Axel Klenk830
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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 5 weeks ago by Axel Klenk830
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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 5 weeks ago by Axel Klenk830
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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 11 weeks ago by Axel Klenk830
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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 3 months ago by Axel Klenk830
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Answer: A: Subsetting GSE data with information from two different slots
... Dear A, like any subsetting in R, e.g.: sub <- es[, es$source_name_ch1 == "liver" & es$description == "primary cells, normal"] Rather a question for R-help or StackOverflow. HTH,  - axel   ...
written 3 months ago by Axel Klenk830
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Answer: A: Cannot read Biom file
... Hi Channen1221, we need a little bit of information to help you. First of all, please show us the command(s) you have entered. Attaching the output of sessionInfo() is also a good idea. Cheers,  - axel ...
written 3 months ago by Axel Klenk830
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Answer: A: problems in reading a file in AgiMicroRna package
... Dear Neela, Agilent's reduced output is lacking the 'gMeanSignal' column and this will cause an issue. I'm not sure it is the source of your problem, though, since I'd expect it to affect *all* files rather than just the 13th. You can inspect the source code of AgiMicroRna::readMicroRnaAFE by typi ...
written 4 months ago by Axel Klenk830
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Answer: A: Package: AgiMicroRna; Error in Loading the file
... Dear neelakandanbt, the first message indicates that package 'S4Vectors' is not installed.  You need to install it before you can continue. Please follow the instructions here: https://bioconductor.org/install/ on how to install Bioconductor packages.  I'd expect the second issue to go away once ...
written 4 months ago by Axel Klenk830
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Answer: A: Why can't I use the same R package to get the same conclusions as the author?
...   The package version(s) are important, too, as the software evolves. System libraries such as BLAS and LAPACK may cause differences. Exactly reproducing such an analysis is not easy. ...
written 6 months ago by Axel Klenk830

Latest awards to Axel Klenk

Scholar 8 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 22 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 23 months ago, voted at least 25 times.
Teacher 3.1 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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