Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
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EMBL European Molecular Biology Laboratory
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Posts by Wolfgang Huber

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Job: Computational 4D and single-cell expression analysis of animal development and regeneration
... A joint postdoctoral project is planned by the groups of Aissam Ikmi and Wolfgang Huber at EMBL Heidelberg to develop cutting-edge computational approaches at the intersection of developmental and regenerative biology. The goal of the project is to build an integrated ‘big-data’ based quantitative m ...
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Answer: A: IHW scale of problem
... In addition, you can randomly sample your hypotheses with various sample sizes, measure run time using e.g. *system.time* or the *microbenchmark* package, plot time against number of hypotheses, see that the relationship is linear, measure the slope, and predict the run time for your problem size. N ...
written 4 days ago by Wolfgang Huber13k
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Job: Postdoc Position in Computational Single Cell Genetics / Statistical Modeling
... # 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 ...
job embl huber written 3 months ago by Wolfgang Huber13k
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News: Course announcement: Statistical Data Analysis for Genome Scale Biology (CSAMA) - Brixen, Italy 21-26 July 2019
... 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 ...
news csama written 3 months ago by Wolfgang Huber13k
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Answer: A: VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
... 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 3 months ago by Wolfgang Huber13k
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Comment: C: DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what
... 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 3 months ago by Wolfgang Huber13k
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Answer: A: stringasfactor = F changes the output of pheatmap, why?
... 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 4 months ago by Wolfgang Huber13k
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Job: Staff researcher position in Machine Learning - Multimodal data analysis, dimension reduction
... 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. ...
job factor analysis mofa written 4 months ago by Wolfgang Huber13k
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Answer: A: Array quality metrics for large sample size
... 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 4 months ago by Wolfgang Huber13k
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Comment: C: Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(
... 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 4 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Popular Question 6 months ago, created a question with more than 1,000 views. For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 12 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Appreciated 12 months ago, created a post with more than 5 votes. For exprs function - clash with dplyr
Popular Question 12 months ago, created a question with more than 1,000 views. For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq2
Student 13 months ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Scholar 13 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Guru 24 months ago, received more than 100 upvotes.
Appreciated 24 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question 24 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 2.0 years ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.3 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Voter 3.2 years ago, voted more than 100 times.
Scholar 3.2 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Scholar 3.2 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 3.2 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 3.2 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2

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