User: Axel Klenk
Axel Klenk • 770
- Reputation:
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Posts by Axel Klenk
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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 11 days ago by
Axel Klenk • 770
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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 11 days ago by
Axel Klenk • 770
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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 11 days ago by
Axel Klenk • 770
• updated 11 days ago by
Gordon Smyth ♦ 30k
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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.
...
written 8 months ago by
Axel Klenk • 770
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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 10 months ago by
Axel Klenk • 770
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... Hi James, thanks for the hint, will do it that way next time.
...
written 10 months ago by
Axel Klenk • 770
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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 10 months ago by
Axel Klenk • 770
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... Hi all,
I'm afraid I have hit the same or a similar issue when trying to rebuild one of my annotation packages today. The script has worked 2015-08-17 but unfortunately throws an error now, on ubuntu, using up-to-date versions. I'm grateful for any help
I have run:
library("AnnotationForge")
pkg ...
written 10 months ago by
Axel Klenk • 770
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Comment:
C: Limma Elist subsetting
... sorry for not checking my answer... data$E is a matrix and not a vector...
so, exactly what do you want to subset? only rows with all values >= 2.3, e.g.
data[apply(data$E, 1, function(x) all(x >= 2.3)), ]
should do that; and there is package genefilter for more complicated things.
...
written 11 months ago by
Axel Klenk • 770
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Answer:
A: Limma Elist subsetting
... data$E >= 2.3
specifies the rows you want to select but you need to specify the columns as well. If you want all columns:
data[data$E >= 2.3, ]
notice the "," -- one-character error :-)
Cheers,
- axel
...
written 11 months ago by
Axel Klenk • 770
Latest awards to Axel Klenk
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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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