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 • 1,340 results • page 1 of 134 • next >
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Answer: A: Found more than one class
... FWIW this appears to be related to a bug in class handling in an older (outdated) version of R, which Michael or someone recently fixed: https://stat.ethz.ch/pipermail/bioc-devel/2016-April/009142.html https://cran.r-project.org/doc/manuals/r-release/NEWS.html (CHANGES IN R 3.3.2, Section Bug Fi ...
written 14 hours ago by Wolfgang Huber13k
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Answer: A: Running DESeq2 with gene-dependent binary variable such as membership in pathway
... Using gene-dependent covariates can make sense - not for DESeq2 per se, but for the subsequent multiple testing analysis. Have a look at the IHW package and its associated paper. In this way, you can take advantage of the fact that the prior probability of being differentially expressed is quite dif ...
written 15 hours ago by Wolfgang Huber13k
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Comment: C: Found more than one class
... What is your devtools::session_info() ? ...
written 7 days ago by Wolfgang Huber13k
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Comment: C: By pass dispersion estimation in DESeq2
... If this is becoming a frequent enough use case, could the above (first code chunk) be exposed as an option in the DESeq() wrapper? ...
written 13 days ago by Wolfgang Huber13k
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Answer: A: expression matrix with varianceStabilizingTransformation
... Dear lirongrossmann The transformation parameters depend on the statistical distribution of the data, so it is to be expected that the transformation changes (a bit) if data are added or removed, especially if these make replicate variances look higher or lower. If your goal is sorting genes by ov ...
written 5 weeks ago by Wolfgang Huber13k
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Comment: C: Problem installing rhdf5
... For good measure, try with a more recent version of R and perhaps also update the rest of your system before hunting quirks of a possibly obsolete system configuration. There is a couple of oddities, e.g. "installation path not writeable, unable to update packages: boot, ... survival" (problem with ...
written 7 weeks ago by Wolfgang Huber13k
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Answer: A: function getAE from ArrayExpress needs update because EBI has switched to https
... I was informed by the ArrayExpress package maintainer Ugis Sarkans that they plan to restore http access to ArrayExpress APIs. ...
written 7 weeks ago by Wolfgang Huber13k
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Comment: C: DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... Hi Komal Can you please post (a public URL to) the data objects countFiles, flattenedFile, sampleTable the code that produces them the output of devtools::session_info() This should make it easier to troubleshoot what is going on. (Check out the advice in the Bioconductor posting guide, whic ...
written 7 weeks ago by Wolfgang Huber13k
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Answer: A: Different PCA plots using rlog and vsd on the same data set
... Can you try with selecting the top 100 (or 200, 500) genes, by baseMean? Or also by rowVars of dds, vsd. When you apply PCA to all genes, the 'signal' may be dominated by precarious variations in the many genes with low counts. Please also try posting the PCA plots. ...
written 8 weeks ago by Wolfgang Huber13k
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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 11 weeks 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 9 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 9 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 21 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 8.4 years ago, created more than 1,000 posts (questions + answers + comments).

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