User: Axel Klenk
Axel Klenk • 790
- Reputation:
- 790
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- Location:
- Switzerland
- Last seen:
- 6 hours ago
- Joined:
- 8 years, 8 months ago
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Posts by Axel Klenk
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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.
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written 5 weeks ago by
Axel Klenk • 790
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Hello,
GPL570 is Affy HG-U133+2 and to my knowledge these are always single color.
Cheers,
- axel
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written 12 weeks ago by
Axel Klenk • 790
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... Dear rkp,
what's "correct" or "better" depends on your definition of DEG but if you require a certain
logFC and a certain p-value, have a look at function treat(), also in the limma package.
?treat
Cheers,
- axel
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written 3 months ago by
Axel Klenk • 790
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... Ok, I have downloaded that file and taken a look at it and it is not Agilent format at all :-( but
rather a tab-delimited textfile with one column <slide_id>_<array_position>.txt:gProcessedSignal
per sample.
You *could* try to read it using read.delim() but I do not see any advantage ...
written 4 months ago by
Axel Klenk • 790
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... GSE85426 appears to be Cy3/green only. Have you tried
x <- read.maimages("GSE85426_raw_data.txt",source="agilent", green.only = TRUE)
?
...
written 4 months ago by
Axel Klenk • 790
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... Dear annecomplete,
don't try too many packages -- the complete analysis can be done with limma.
Unfortunately, you do not give us your call to read.maimages() and we don't know which columns it cannot find in your Agilent files. At some point, Agilent introduced a reduced ("lean" IIRC) file format ...
written 4 months ago by
Axel Klenk • 790
• updated 4 months ago by
Gordon Smyth ♦ 31k
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Hello,
simply continue following the user's guide until you find limma's topTable() function
and make sure to read its help page to learn how to sort your results.
HTH.
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written 12 months ago by
Axel Klenk • 790
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... Dear Thomas,
hmm, just an idea -- are you sure that targets$FileName is a character, not a factor?
What does str(targets) say about this?
As the error message claims the problem is with file.exists -- what's the result of
file.exists(targets$FileName)
?
Cheers,
- axel
...
written 14 months ago by
Axel Klenk • 790
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... Hi James, thanks for the hint, will do it that way next time.
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written 14 months ago by
Axel Klenk • 790
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... Hi again,
this is resolved by simply installing the rat.db0 package that was missing on my new PC. The vignette explains clearly that one needs it and why one needs it and I'm sure I have read it last year when I wrote that script -- but not now before re-running it. :-(
(While it's clearly my fau ...
written 14 months ago by
Axel Klenk • 790
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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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