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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Last seen:
1 day, 11 hours ago
Joined:
14 years, 8 months ago
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Posts by Wolfgang Huber

<prev • 1,296 results • page 1 of 130 • next >
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Comment: C: Error in Gviz | IdeogramTrack
... unit tests? ...
written 5 days ago by Wolfgang Huber12k
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Comment: C: Error in Gviz | IdeogramTrack
... I was bitten by the same - and in addition, wonder whether this (currently unresolved) issue could also be due to a correlated set of updates at the UCSC website? https://support.bioconductor.org/p/92504/ ...
written 5 days ago by Wolfgang Huber12k
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Answer: A: Unable to install DeSeq2 and EdgeR in ubuntu 16.04 , this is what happens when I
... Have a look at the error message /usr/bin/ld: cannot find -lgfortran and try again after installing a fortran compiler.     ...
written 11 days ago by Wolfgang Huber12k
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Answer: A: Questions about SomaticSignatures packages
... Hi Zzsu Your question is a bit open-ended, so the best I can say at this point is to recommend having a look at the accompanying paper https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv408 and perhaps you'll also benefit from familiarizing yourself with matrix dec ...
written 12 days ago by Wolfgang Huber12k
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Answer: A: Bug in vsn2 in package vsn?
... Dear Peter Thank you for pointing this out and the clear bug report. This should be fixed in the devel branch in vsn >= 3.43.9, which is in the subversion repository now and should be online in a couple of days. As the vsn2 function's manual page says, the calib="none" option is an experimental ...
written 12 days ago by Wolfgang Huber12k
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Comment: C: S4Vectors masks/breaks regular Matrix functions
... The size of the installed Matrix package on my system (MacOS) is 5.8M, the load time is ~1.5sec, and most users don't compile but install binaries - so, compared to everything else we are lugging around in BioC I wonder how bad just having BiocGenerics depend on Matrix would really be...? ...
written 12 days ago by Wolfgang Huber12k
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Comment: C: Why does rlog and vst use normalized counts?
... Re peculiarities of single cell data: "...you often have genes which are mostly 0's but then highly expressed in a minority of cells": these are likely not really highly expressed genes, but rather, low expressed ones that just happen to have gotten highly (PCR)-amplified in a few cells. That al ...
written 8 weeks ago by Wolfgang Huber12k
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Answer: A: Best practices for converting adj matrix -> graphNEL
... Dear Bryon I am not sure there is "the intended method". Most of the code in this package is >10 years old, and it was contributed by several authors at the time. So, contributions and patches from you will also be welcome. Some observations that might be useful: as(adj, "graphNEL") with adj ...
written 9 weeks ago by Wolfgang Huber12k
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Job: PhD-level staff position in computational modelling and quantitative biology at EMBL
... Computational Biologist (mathematical modelling) Location: Heidelberg, Germany Staff Category: Staff member Contract Duration: 3 years Grading: 6, 7 or 8; depending on qualification and experience Closing Date: 18 January 2017 ...
modelling job exciting written 9 weeks ago by Wolfgang Huber12k
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Answer: A: how to change color of points log2foldchange>1
... Use this xs <- x[x$baseMean>1, ] plotMA(xs, col = ifelse(xs$log2FoldChange>1, "red", "gray")) ...
written 9 weeks ago by Wolfgang Huber12k

Latest awards to Wolfgang Huber

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Voter 10 months ago, voted more than 100 times.
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Scholar 10 months ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 10 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 10 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 12 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 13 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 14 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: rounding issues using the VSN package
Scholar 19 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
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Scholar 2.2 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 2.4 years ago, created 100 posts.
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