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:
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Posts by Wolfgang Huber

<prev • 1,314 results • page 1 of 132 • next >
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Answer: A: Save multiple plots into single pdf from Deseq2 analysis?
... You say "i was not succesful" but not really what you consider your problem is... However, I'd recommend taking a much better approach, namely use Rmarkdown (or knitr) to prepare your analysis script, and use PDF as the output format.   ...
written 7 days ago by Wolfgang Huber13k
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Comment: C: EBImage cannot read .png images from Image.R
... Can you please post a (minimal) code example make sure you use recent package versions, and provide the output of devtools::session_info() ? ...
written 7 days ago by Wolfgang Huber13k
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Comment: C: find fold change in DESeq2 results
... See also R FAQ 7.31 https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f ...
written 10 days ago by Wolfgang Huber13k
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Answer: A: Application of Deseq2 to mass spec data
... I don't think I know all the different varieties of MS data, but for many quantitative MS data types, it is appropriate to treat them as continuous measurements on which you can use ordinary statistical models and tests, possibly with empirical Bayes moderation (limma) and/or suitable transformation ...
written 20 days ago by Wolfgang Huber13k
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Comment: C: Nonspecific filtering of microarray data
... Why do you think that? "need" is a strong term, but filtering (or weighting, see my reply below) can improve an analysis by giving better power. ...
written 20 days ago by Wolfgang Huber13k
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Answer: A: Nonspecific filtering of microarray data
... In many cases, using data-driven weights for the multiple testing computation is a better approach than yes/no filtering, see e.g. the IHW vignette and the associated paper. The vignette also gives hints on the choice of the weighting covariate and diagnostic plots.   ...
written 20 days ago by Wolfgang Huber13k
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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 6 weeks 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 8 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 8 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 9 weeks ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Scholar 15 days ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 3 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 3 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 14 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 14 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: How is the mean-variance plot calculated?
Scholar 14 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 14 months ago, voted more than 100 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 18 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 23 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 2.1 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 2.8 years ago, created 100 posts.
Oracle 7.9 years ago, created more than 1,000 posts (questions + answers + comments).

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