Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
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EMBL European Molecular Biology Laboratory
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http://www.embl.de/res...
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Posts by Wolfgang Huber

<prev • 1,331 results • page 1 of 134 • next >
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Answer: A: phyloseq heatmap blank after multiple package updates
... Can you post a minimal working example (with all the code) to reproduce your problem, also the input data (can be "made up") and an example output file (.png, .pdf)? This is most likely the precondition for a specific and helpful reply.. ...
written 16 days ago by Wolfgang Huber13k
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Answer: A: Error with DESeqDataSetFromMatrix is not available (for R version 3.4.1)
... DESeqDataSetFromMatrix is not a package. There is a package called DESeq2, and its documentation is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
written 27 days ago by Wolfgang Huber13k
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Comment: C: DESeq2: How to manually perform filtering and outlier detection?
... Btw, there is now an (even better) alternative to independent filtering: independent hypothesis weighting, IHW. ...
written 6 weeks ago by Wolfgang Huber13k
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Answer: A: DESeq2: How to manually perform filtering and outlier detection?
... Heikki First, it'll be good to clarify concepts regarding outlier removal: removing genes whose data do not appear to fit the mathematical model used by DESeq2 (it's called a "gamma-Poisson generalized linear model") and your design matrix independent filtering: removing genes whose data perfec ...
written 6 weeks ago by Wolfgang Huber13k
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Answer: A: Filtering low intensity probes in microarray data
... Have a look at the IHW package, with overall variance (blind w.r.t. design factors) as a covariate. See also the accompanying paper. ...
written 8 weeks ago by Wolfgang Huber13k
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Answer: A: Volcanoplot with limma - RAW P-values or Adj.P-Values
... There's another reason to support Gordon's view. There is a fundamental difference between p-values and FDR: p-values are per-hypothesis (i.e., per-gene) properties, whereas FDR is an average across all rejected hypotheses. I.e., if you have a set of hypotheses (genes) rejected at a certain FDR $\al ...
written 8 weeks ago by Wolfgang Huber13k
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Tutorial: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
... Here's a few notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26 Writing papers in Rmarkdown, BiocStyle... (and books, posters)   Multi-panel figures CRAN package multipanelfigure   Tables knitr:  kable (ideally if you then also define your own CSS); xtable ...
biocstyle tutorial rmarkdown written 8 weeks ago by Wolfgang Huber13k
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Comment: C: markdown is coming to the support site
... Thanks, this is great! As was asked at the Bioc-Devel Meeting, could there be support for math markdown? E.g. $$ \int_{-\infty}^{+\infty}f(x)\;\mathrm{d}x $$ \[ \int_{-\infty}^{+\infty}f(x)\;\mathrm{d}x \] ...
written 8 weeks ago by Wolfgang Huber13k
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Comment: C: Duplicated author affiliations in BiocStyle-based HTML document
... I can reproduce this. Andrzej is away until Wednesday. It seems possible that the problem has to do with code in BiocStyle/R/auth_affil.R. ...
written 9 weeks ago by Wolfgang Huber13k
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Comment: C: DESeq2 installing error: S4Vectors cannot be unloaded; anyone?
... Why don't you want to update to a newer R (e.g. 3.4.1 is current)? ...
written 10 weeks ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Scholar 3 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 6 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 17 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 17 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 17 months ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 17 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 17 months ago, voted more than 100 times.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 19 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 20 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 21 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.2 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 2.2 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 2.3 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 3.0 years ago, created 100 posts.
Oracle 8.2 years ago, created more than 1,000 posts (questions + answers + comments).

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