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Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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- EMBL European Molecular Biology Laboratory
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- http://www.embl.de/res...
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- Joined:
- 16 years, 8 months ago
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Posts by Wolfgang Huber
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... It's impossible to say for sure without you giving reproducible code, but expressions like this are dangerous
```
assay(vsdyear)[ immune_genes_paper$Gene_ID, ...]
```
if `Gene_ID` can either be a character vector or a factor. Namely, if `Gene_ID` is a factor, it is converted to an integer vector c ...
written 10 days ago by
Wolfgang Huber ♦ 13k
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... Visit the EMBL Job site: https://www.embl.de/jobs/searchjobs/index.php?ref=HD01466
The research groups of Wolfgang Huber at EMBL and Oliver Stegle at DKFZ and EMBL, located in Heidelberg, work on machine learning and statistical computing solutions for cutting-edge biology and biomedicine research. ...
written 18 days ago by
Wolfgang Huber ♦ 13k
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... Have a look at the vignette *Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output of the package*. You could eliminate certain parts of the report that take a very a long time, or write code to parallelize them. ...
written 21 days ago by
Wolfgang Huber ♦ 13k
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... The warning message you quote cannot have been generated from a recent version of `arrayQualityMetrics`, see e.g. [https://github.com/grimbough/arrayQualityMetrics/blob/master/R/makeColors.R][1]. Are you sure you are not using an older version of the package?
[1]: https://github.com/grimbough/ar ...
written 21 days ago by
Wolfgang Huber ♦ 13k
0
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39
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... It is possible that https://www.huber.embl.de/msmb/Chap-Images.html#sec:segbin answers your question.
I.e, from the output of `table`, you get the sizes of the regions, and then you can select them based on the values in the output of `bwlabel`. ...
written 21 days ago by
Wolfgang Huber ♦ 13k
0
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1
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48
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Answer:
A: EBimage fftw issue
... I think your problem can be reduced to properly installing the `fftwtools` package for R from CRAN (https://cran.r-project.org/web/packages/fftwtools/index.html) on your cluster. `EBImage` imports this package, but your problem is at the level of `fftwtools`, not of `EBImage`.
Installation of the ...
written 24 days ago by
Wolfgang Huber ♦ 13k
1
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121
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... Consulting and teaching statistical data analysis in fundamental biology research.
- https://www.embl.de/jobs/searchjobs/index.php?ref=HD01456&newlang=1&loc
- https://bio-it.embl.de/centres/csda/
EMBL is an international research organization covering many fields of modern biology. Five ...
written 6 weeks ago by
Wolfgang Huber ♦ 13k
2
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126
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... Have a look at the manual pages of these functions. The first sentence of that for varianceStabilizingTransformation says "This function calculates a variance stabilizing transformation (VST) from the fitted dispersion-mean relation(s) and then transforms the count data (normalized by division by th ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
0
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1
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85
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1
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Answer:
A: DESeq2: plotMA looks wrong
... Why do you round the values (line countData = round(x,0))? DESeq2 works on the raw counts, which are integers. If you give it something else, then garbage-in / garbage-out.
Suppose you are feeding it actual read counts, then one possible explanation is that the default DESeq "normalization" does n ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
0
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1
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179
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... I don't know how to get this to work with GNU binutils. The authoritative source on recommended build configuration is probably https://www.bioconductor.org/checkResults/release/bioc-LATEST/merida1-NodeInfo.html .
On my notebook with MacOS Mojave, R itself and the lypsymphony package build from sou ...
written 11 weeks ago by
Wolfgang Huber ♦ 13k
Latest awards to Wolfgang Huber
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
8 months ago,
created an answer that has been accepted.
For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Appreciated
8 months ago,
created a post with more than 5 votes.
For exprs function - clash with dplyr
Popular Question
8 months ago,
created a question with more than 1,000 views.
For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Student
9 months ago,
asked a question with at least 3 up-votes.
For exprs function - clash with dplyr
Scholar
9 months ago,
created an answer that has been accepted.
For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Course announcement: CSAMA 2015 (13th ed.) Statistics and Computing in Genome Data Science
Guru
20 months ago,
received more than 100 upvotes.
Appreciated
20 months ago,
created a post with more than 5 votes.
For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Postdocs in Computational Biology / Statistical Data Analysis at EMBL and Univ. Hospital Heidelberg: mechanisms of drug response from ex-vivo large-scale drug testing and multi-omics in cancer
Scholar
20 months ago,
created an answer that has been accepted.
For A: Nonspecific filtering of microarray data
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher
24 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Teacher
24 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
24 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: Processing imaging data from high throughput compound screen with EBImage
Voter
2.8 years ago,
voted more than 100 times.
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: How is the mean-variance plot calculated?
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
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