Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... 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 Huber ♦ 13k
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... 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 Huber ♦ 13k
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... Have you tried simply row-subsetting the DESeqDataSet before calling the model fitting functions?
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written 13 days ago by
Wolfgang Huber ♦ 13k
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... 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.
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written 24 days ago by
Wolfgang Huber ♦ 13k
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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.
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written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... When you say "What I want is", what is the basis for this desire?
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written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... 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.
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written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... See also https://github.com/satijalab/seurat/issues/485 and https://github.com/satijalab/seurat/pull/487
...
written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... 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 ...
written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... 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 ...
written 4 weeks ago by
Wolfgang Huber ♦ 13k
Latest awards to Wolfgang Huber
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
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 Postdocs in Computational Biology / Statistical Data Analysis at EMBL and Univ. Hospital Heidelberg: mechanisms of drug response from ex-vivo large-scale drug testing and multi-omics in cancer
Appreciated
12 months ago,
created a post with more than 5 votes.
For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Course announcement: CSAMA 2015 (13th ed.) Statistics and Computing in Genome Data Science
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 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
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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
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2.3 years ago,
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For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
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2.5 years ago,
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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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