User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk790
Reputation:
790
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Trusted
Location:
Switzerland
Last seen:
6 hours ago
Joined:
8 years, 8 months ago
Email:
a*********@idorsia.com

Posts by Axel Klenk

<prev • 97 results • page 1 of 10 • next >
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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 5 weeks ago by Axel Klenk790
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Answer: A: How to know which Microarray Technique was used to processes the files
...   Hello, GPL570 is Affy HG-U133+2 and to my knowledge these are always single color. Cheers,  - axel   ...
written 12 weeks ago by Axel Klenk790
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Answer: A: Identification of DEGs through limma analysis
... 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 3 months ago by Axel Klenk790
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Comment: C: Help with diff. expression analysis of Agilent files
... 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 Klenk790
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Comment: C: Help with diff. expression analysis of Agilent files
... 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 Klenk790
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Answer: A: Help with diff. expression analysis of Agilent files
... 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 Klenk790 • updated 4 months ago by Gordon Smyth31k
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Answer: A: limma decideTests results; how to get/sort most significant Genes?
...   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 12 months ago by Axel Klenk790
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Answer: A: Error message when trying to use the 'Align' function of the 'Rsubread' package
... 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 Klenk790
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Comment: C: sqliteSendQuery error in AnnotationForge bioconductor package
... Hi James, thanks for the hint, will do it that way next time. ...
written 14 months ago by Axel Klenk790
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Comment: C: sqliteSendQuery error in AnnotationForge bioconductor package
... 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 Klenk790

Latest awards to Axel Klenk

Scholar 3 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 17 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 18 months ago, voted at least 25 times.
Teacher 2.7 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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