Moderator: Wolfgang Huber

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

<prev • 1,338 results • page 2 of 134 • next >
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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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 4 months 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 4 months ago by Wolfgang Huber13k
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Answer: A: FourCSeq - errors in plotZScores
... Rustavo please first update your R, and use biocLite to install all needed packages. Just to avoid that you're suffering from version mismatches between your installed packages, or that your particular problem has already been fixed. Wolfgang   ...
written 4 months ago by Wolfgang Huber13k
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Comment: C: Error message that there is no package called Biobase
... Your R version (3.1.2) is badly out of date. You'll have more fun with a more recent version, e.g. the current version is 3.4.1, see https://cran.r-project.org/ Also, if you haven't, consider using R-Studio, it makes many things around using R much easier. ...
written 4 months ago by Wolfgang Huber13k
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Answer: A: name of column in R
... You might want to read the R intro, esp. the chapter Reading data from files, and you might enjoy the readr package. ...
written 4 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Scholar 5 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 8 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
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: DESeq2 interacting with agricolae
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 19 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 19 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 19 months ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 19 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 19 months ago, voted more than 100 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 21 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 22 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 23 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.4 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 2.4 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 2.5 years ago, voted at least 25 times.
Scholar 2.9 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 3.2 years ago, created 100 posts.
Oracle 8.3 years ago, created more than 1,000 posts (questions + answers + comments).

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