Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
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EMBL European Molecular Biology Laboratory
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http://www.embl.de/res...
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Joined:
14 years, 11 months ago
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Posts by Wolfgang Huber

<prev • 1,308 results • page 1 of 131 • next >
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Answer: A: AIC-like measure for DESeq2
... You could use cross-validation: fit the model on a subset of the samples,  then apply to the held-out samples and show that prediction performance on these increases. ...
written 18 days ago by Wolfgang Huber13k
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Answer: C: Found consistent padj values for all the samples in DESeq2 R Package
... It appears that your dataset does not yield any evidence for differential expression. So you could use the same data, but make a different comparison, or use a new dataset and make the same comparison. ...
written 4 weeks ago by Wolfgang Huber13k
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Comment: C: DESeq2::DESeq command hangs at "fitting model and testing" step with no output.
... Did you try with using the assignment operator "<-" instead of the comparison "<" in your command line?   ...
written 4 weeks ago by Wolfgang Huber13k
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Answer: A: Where to find open access microbiome data for case-control comparative study?
... Also the curatedMetagenomicData package, http://bioconductor.org/packages/devel/data/experiment/html/curatedMetagenomicData.html ...
written 5 weeks ago by Wolfgang Huber13k
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Comment: C: Error in lfproc(x, y, weights = weights, cens = cens,... : newsplit: out of ver
... Not too large, but too different from what DESeq2 expects. ...
written 5 weeks ago by Wolfgang Huber13k
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Answer: A: Error in lfproc(x, y, weights = weights, cens = cens,... : newsplit: out of ver
... Can you do some exploratory data analysis (EDA) & visualisation to see how the mean-variance relationship of your data looks like? ...
written 5 weeks ago by Wolfgang Huber13k
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Answer: A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
... In addition to Mike's answer, let me add, as a more general comment, that it is always helpful to distinguish between the route taken and the destination, i.e., between the assumptions made to come up with an algorithm for finding a data transformation, and the usefulness of the transformation that ...
written 5 weeks ago by Wolfgang Huber13k
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Comment: C: Tutorial for RNA-Seq Data Analysis
... ... and also https://www.bioconductor.org/help/workflows/rnaseqGene/ ...
written 6 weeks ago by Wolfgang Huber13k
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Answer: A: unusal expression level values after normalization in Affymetrix Microarray expe
... gcrma is a sophisticated and numerically somewhat complex algorithm; it is possible that ties might be induced as you describe. I'd recommend: Trying with plain rma Plotting the data from some of the offending probe set at the per-probe level, e.g. as in Fig.12 of Chapter 3 of the Case Studies ...
written 7 weeks ago by Wolfgang Huber13k
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Comment: C: Deseq2 to nanlyse one level / condition
... Can you talk to the people who went to the expense and effort to create this data set to find out what the objective of creating it was? ...
written 7 weeks ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Popular Question 10 weeks ago, created a question with more than 1,000 views. For DESeq2
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 12 weeks ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 13 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 13 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: How is the mean-variance plot calculated?
Scholar 13 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 13 months ago, voted more than 100 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 15 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 16 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 17 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 22 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 23 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 2.0 years ago, voted at least 25 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 2.7 years ago, created 100 posts.
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