User: Axel Klenk
Axel Klenk • 830
- Reputation:
- 830
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- Trusted
- Location:
- Switzerland
- Last seen:
- 12 hours ago
- Joined:
- 9 years, 4 months ago
- Email:
- a*********@idorsia.com
Posts by Axel Klenk
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... 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 4 months ago by
Axel Klenk • 830
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... Yes, they are fine, you can use them. Keep in mind that they are false discovery rates not p-values.
...
written 4 months ago by
Axel Klenk • 830
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... Dear b.nota,
yes, it is a known effect of the BH p-value adjustment, not limma or voom.
Cheers,
- axel
...
written 4 months ago by
Axel Klenk • 830
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... 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 5 months ago by
Axel Klenk • 830
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... 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 6 months ago by
Axel Klenk • 830
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... 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 6 months ago by
Axel Klenk • 830
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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 6 months ago by
Axel Klenk • 830
0
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... 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 7 months ago by
Axel Klenk • 830
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... 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 7 months ago by
Axel Klenk • 830
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...
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 9 months ago by
Axel Klenk • 830
Latest awards to Axel Klenk
Centurion
11 months ago,
created 100 posts.
Scholar
11 months ago,
created an answer that has been accepted.
For A: Identification of DEGs through limma analysis
Supporter
2.2 years ago,
voted at least 25 times.
Teacher
3.3 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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