User: Axel Klenk
Axel Klenk • 790
- Reputation:
- 790
- Status:
- Trusted
- Location:
- Switzerland
- Last seen:
- 3 hours ago
- Joined:
- 8 years, 6 months ago
- Email:
- a*********@idorsia.com
Posts by Axel Klenk
<prev
• 96 results •
page 1 of 10 •
next >
0
votes
1
answers
66
views
1
answers
...
Hello,
GPL570 is Affy HG-U133+2 and to my knowledge these are always single color.
Cheers,
- axel
...
written 28 days ago by
Axel Klenk • 790
0
votes
4
answers
116
views
4
answers
... 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
...
written 5 weeks ago by
Axel Klenk • 790
0
votes
1
answers
119
views
1
answers
... 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 10 weeks ago by
Axel Klenk • 790
0
votes
1
answers
119
views
1
answers
... GSE85426 appears to be Cy3/green only. Have you tried
x <- read.maimages("GSE85426_raw_data.txt",source="agilent", green.only = TRUE)
?
...
written 10 weeks ago by
Axel Klenk • 790
0
votes
1
answers
119
views
1
answers
... 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 10 weeks ago by
Axel Klenk • 790
• updated 9 weeks ago by
Gordon Smyth ♦ 30k
0
votes
1
answers
202
views
1
answers
...
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 10 months ago by
Axel Klenk • 790
0
votes
2
answers
239
views
2
answers
... 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 12 months ago by
Axel Klenk • 790
0
votes
3
answers
2.5k
views
3
answers
... Hi James, thanks for the hint, will do it that way next time.
...
written 12 months ago by
Axel Klenk • 790
0
votes
3
answers
2.5k
views
3
answers
... 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 12 months ago by
Axel Klenk • 790
0
votes
3
answers
2.5k
views
3
answers
... 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 12 months ago by
Axel Klenk • 790
Latest awards to Axel Klenk
Supporter
16 months ago,
voted at least 25 times.
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: basic R question: concatenate two numeric vectors grouped by element index
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 304 users visited in the last hour