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 • 1,347 results • page 2 of 135 • next >
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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 9 weeks 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 4 months 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 4 months 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 5 months 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 5 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Scholar 7 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 10 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 21 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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 21 months ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 21 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 21 months ago, voted more than 100 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 23 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.0 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.1 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.5 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 2.5 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 2.7 years ago, voted at least 25 times.
Scholar 3.1 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 3.3 years ago, created 100 posts.
Oracle 8.5 years ago, created more than 1,000 posts (questions + answers + comments).

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