Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
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Posts by Wolfgang Huber

<prev • 1,298 results • page 1 of 130 • next >
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Answer: A: statistical tests to show the specificity of a phenomenon (eg increase in H3K27m
... Bogdan The main point is: don't use a test, or the language and concepts of testing here. Rejecting a null hypothesis of non-specificity is near to uninformative (boring, besides the point, ridiculous, ...) with regard to the strength of specificity, since such a hypothesis test would confound effe ...
written 4 weeks ago by Wolfgang Huber12k
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Answer: A: Getting error like Could not find column(s) 'rel_fc_Replication'
... Mohammed You will need to provide sessionInfo complete, self-contained example code? Please do follow the posting guide. Wolfgang   ...
written 5 weeks ago by Wolfgang Huber12k
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Comment: C: Error in Gviz | IdeogramTrack
... unit tests? ...
written 5 weeks 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 weeks 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 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks 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 3 months 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 3 months ago by Wolfgang Huber12k

Latest awards to Wolfgang Huber

Popular Question 18 days ago, created a question with more than 1,000 views. For DESeq2
Popular Question 18 days ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 4 weeks ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 4 weeks 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: Processing imaging data from high throughput compound screen with EBImage
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 11 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 11 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 11 months ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 11 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 15 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 21 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 21 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
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Scholar 2.3 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
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