User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk820
Reputation:
820
Status:
Trusted
Location:
Switzerland
Last seen:
50 minutes ago
Joined:
8 years, 10 months ago
Email:
a*********@idorsia.com

Posts by Axel Klenk

<prev • 102 results • page 1 of 11 • next >
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Answer: A: No differential expression with limmaCtData possible
... 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 1 day ago by Axel Klenk820
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Answer: A: Subsetting GSE data with information from two different slots
... 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 13 days ago by Axel Klenk820
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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 19 days ago by Axel Klenk820
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Answer: A: problems in reading a file in AgiMicroRna package
... 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 6 weeks ago by Axel Klenk820
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Answer: A: Package: AgiMicroRna; Error in Loading the file
... 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 6 weeks ago by Axel Klenk820
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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 3 months ago by Axel Klenk820
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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 4 months ago by Axel Klenk820
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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 5 months ago by Axel Klenk820
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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 6 months ago by Axel Klenk820
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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 6 months ago by Axel Klenk820

Latest awards to Axel Klenk

Scholar 4 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 19 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 20 months ago, voted at least 25 times.
Teacher 2.8 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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