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 • 1,367 results • page 1 of 137 • next >
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Answer: A: How to filter overlaping EBImage objects?
... How about overlap <- (red > 0) & (green > 0) This finds overlapping pixels. If you want to look at cells, you'll need to segment the red image into cells, and subset those cells that overlap in a similar manner. ...
written 26 days ago by Wolfgang Huber13k
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Answer: A: DESeq2- Size factors (median of ratios) assumptions - global adjustment normaliz
... On a more philosophical note, the question "which genes are differentially expressed?" that methods like DESeq2 are trying to answer, is scientifically most meaningful if the answer is relatively sparse, and identifying such genes bears some degree of information content. If almost everything is dif ...
written 4 weeks ago by Wolfgang Huber13k
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Answer: A: What are the different strategies to filter out low count genes?
... Besides the reasons that Mike mentioned (save memory or compute time) another motivation for filtering can be to improve your multiple testing computations; if that is the motivation, then in fact, you might better off not filtering, but weighting, as e.g. in https://bioconductor.org/packages/releas ...
written 3 months ago by Wolfgang Huber13k
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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 4 months 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 4 months 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 4 months 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 4 months 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 months 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 months 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 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Appreciated 4 months ago, created a post with more than 5 votes. For exprs function - clash with dplyr
Popular Question 4 months ago, created a question with more than 1,000 views. For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Scholar 4 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Student 5 months ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Popular Question 5 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Guru 15 months ago, received more than 100 upvotes.
Appreciated 15 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 16 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 19 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2
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: DESeq2 interacting with agricolae
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Voter 2.5 years ago, voted more than 100 times.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.5 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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.5 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 2.5 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae

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