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 • 1,364 results • page 1 of 137 • next >
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Answer: C: Anomal pvalue distribution and qvalue calculation
... 1. It looks curious that the three very lowest histogram bins are shorter than some of the higher ones. Maybe this just happened by chance, but it's untypical for the density of p for alternatives to be non-monotonous, and I'd check the source of these p-values. 2. The qvalue result looks fine. For ...
written 10 days ago by Wolfgang Huber13k
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Comment: C: Need to read in DEXSeqResults object to R from csv
... The most common and recommended way to save R objects, move them to a different computer and open them there again are the save and load functions in R. It looks like that the CSV file you saved from the cluster only contains part of the DEXSeqResults object, and what you loaded is not a DEXSeqResul ...
written 11 days ago by Wolfgang Huber13k
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Comment: C: rlog, lfcShrink and vst on gene subset
... Have you tried simply row-subsetting the DESeqDataSet before calling the model fitting functions? ...
written 13 days ago by Wolfgang Huber13k
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Answer: A: Using DESeq2 normalisation method on a tximport list of matrices without sample
... A1. Yes. Try giving a trivial dataframe for colData and a trivial design (like ~1) for design. A2. I'd rather use the estimateSizeFactorsForMatrix for that alternative. A3. No. The normalization methods of DESeq2 and DESeq are (up to implementation details) the same. ...
written 24 days ago by Wolfgang Huber13k
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Comment: C: Relabelling objects - EBImage
... When I just tried (Wed May 23 13:40:08 CEST 2018), I still get a window asking me to "Log in to figshare" when I follow the link in your post. As Andrzej says, a method of providing these files that does not require others to login somewhere would be preferable.   ...
written 4 weeks ago by Wolfgang Huber13k
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Comment: C: [DESeq2] Different results from tutorial
... When you say "What I want is", what is the basis for this desire? ...
written 4 weeks ago by Wolfgang Huber13k
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Answer: A: [DESeq2] Different results from tutorial
... Did you do already do what the output suggests? i.e. [1] see 'cooksCutoff' argument of ?results [2] see 'independentFiltering' argument of ?results Since this seems to be one, if not the, cause of the difference between your outputs.     ...
written 4 weeks ago by Wolfgang Huber13k
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Comment: C: Conversion to SingleCellExperiment from Seurat objects
... See also https://github.com/satijalab/seurat/issues/485 and https://github.com/satijalab/seurat/pull/487 ...
written 4 weeks ago by Wolfgang Huber13k
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Conversion to SingleCellExperiment from Seurat objects
... I realize this is slightly out of scope since Seurat 2.3 is on CRAN, not Bioconductor, but given its developers recent interactions with the SIngleCellExperiment developers, I hope it's OK to post this here:   When trying to convert one of the Seurat data objects from the tabula muris, I get the f ...
seurat singlecellexperiment written 4 weeks ago by Wolfgang Huber13k
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exprs function - clash with dplyr
... I wanted to highlight a recent1 change in the dplyr package that is likely to break a lot of people's existing code. That package now exports2 a function named exprs, which masks a function of the same name from the Biobase package. The latter tends to be used frequently in conjunction with Expr ...
biobase dplyr exprs written 4 weeks ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Popular Question 5 weeks ago, created a question with more than 1,000 views. For DESeq2
Student 5 weeks ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2
Appreciated 12 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Guru 12 months ago, received more than 100 upvotes.
Scholar 12 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 15 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 16 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.2 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.2 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.2 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.2 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 2.2 years ago, voted more than 100 times.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 2.3 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.5 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.5 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2

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