Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... # Postdoctoral Fellow in Computational Single Cell Genetics
**About the team:** The research group of Wolfgang Huber at EMBL works on biological data science and mathematical/computational method development. The interdisciplinary and international team has strong collaborations with researchers i ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
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... We invite you to participate in this year's edition of the summer course **Statistical Data Analysis for Genome Scale Biology** in beautiful Brixen, Italy, from 21-26 July 2019. Course programme and more info are here: https://www.huber.embl.de/csama2019
Confirmed faculty include
- Vincent J. Car ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
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... A thoughtful approach to differential detection for label-free (LFQ) mass spec data is Constantin Ahlmann-Eltze's and Simon Anders' proDD. It explicitly takes into account and models the non-detections. The current state of this work is here: https://github.com/const-ae/proDD and I understand this i ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
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... Marc: one thing you could do in addition to the mean-sd plots is look at MA-plots of pairs of samples: i.e., sample many pairs out of all possible pairs randomly, or look especially at replicates or very similar samples. ...
written 8 weeks ago by
Wolfgang Huber ♦ 13k
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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 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by
Wolfgang Huber ♦ 13k
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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 11 weeks ago by
Wolfgang Huber ♦ 13k
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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 12 weeks ago by
Wolfgang Huber ♦ 13k
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