Moderator: Wolfgang Huber

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

<prev • 1,374 results • page 1 of 138 • next >
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Answer: A: Installing lpsymphony on Mac OS X
... 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 8 days ago by Wolfgang Huber13k
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Comment: C: DEXSeqHTML getListElement GRanges error
... Lance, this "smells" like a version mismatch problem with the particular instance of R and Bioconductor packages (DEXSeq and its various dependencies) you are using. It's hard to say more or diagnose such things remotely. Can you do one (or both) of the following? create a minimal working example ...
written 21 days ago by Wolfgang Huber13k
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Comment: C: IHW multiple testing correction
... --- title: "Lara Urban IHW question 2018-11-18" author: "Wolfgang Huber" output: BiocStyle::html_document: toc_float: TRUE --- # Setup ```{r global_options, include = FALSE} knitr::opts_chunk$set(cache = TRUE, autodep = TRUE) options(error = recover) ``` ```{r message = FALSE} library("IHW ...
written 21 days ago by Wolfgang Huber13k
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Answer: A: IHW multiple testing correction
... Dear Lara Thanks for the clear posting (reproducible script with small working example, post of the plots). Indeed it looks like your variable var is not informative on power or prior probability of the tests that generate your p-values. One can glean this from the plot of -log10(p) over rank(var) ...
written 21 days ago by Wolfgang Huber13k
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Comment: C: IHW multiple testing correction
... The second link should be https://imgur.com/a/prGaWnL - no right parenthesis. ...
written 21 days ago by Wolfgang Huber13k
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Answer: A: Initial List of Deprecated Package Bioc 3.9
... RFC: I have a question regarding best practice for packages like PGPC, which provides not a general-purpose resource, but a reproducible transcript of the (complete) set of analyses presented in a specific, singular paper (in the case of PGPC, published 2015). That means that it's important for the ...
written 4 weeks ago by Wolfgang Huber13k
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News: Ascona Workshop 2019 - Statistical Challenges in Medical Data Science, 16-21 June 2019
... Save the date! We would like to announce and invite you to the workshop on Statistical Challenges in Medical Data Science, to be held on 16 – 21 June 2019 at Monte Verità, Ascona, Switzerland. The purpose of the workshop is to bring together participants from statistics, computational sciences, bio ...
news workshop written 6 weeks ago by Wolfgang Huber13k
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Answer: A: How to filter overlaping EBImage objects?
... How about overlap <- (red > 0) & (green > 0) This finds overlapping pixels. If you want to look at cells, you'll need to segment the red image into cells, and subset those cells that overlap in a similar manner. ...
written 11 weeks ago by Wolfgang Huber13k
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Answer: A: DESeq2- Size factors (median of ratios) assumptions - global adjustment normaliz
... On a more philosophical note, the question "which genes are differentially expressed?" that methods like DESeq2 are trying to answer, is scientifically most meaningful if the answer is relatively sparse, and identifying such genes bears some degree of information content. If almost everything is dif ...
written 12 weeks ago by Wolfgang Huber13k
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Answer: A: What are the different strategies to filter out low count genes?
... Besides the reasons that Mike mentioned (save memory or compute time) another motivation for filtering can be to improve your multiple testing computations; if that is the motivation, then in fact, you might better off not filtering, but weighting, as e.g. in https://bioconductor.org/packages/releas ...
written 5 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Appreciated 6 months ago, created a post with more than 5 votes. For exprs function - clash with dplyr
Popular Question 6 months ago, created a question with more than 1,000 views. For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Scholar 6 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Student 6 months ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 6 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Guru 17 months ago, received more than 100 upvotes.
Appreciated 17 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 18 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 21 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 21 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Voter 2.6 years ago, voted more than 100 times.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.6 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.6 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.6 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 2.6 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae

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