Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... 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 5 weeks ago by
Wolfgang Huber ♦ 13k
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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 9 weeks 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 9 weeks 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 9 weeks 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 11 weeks 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 12 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 12 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 12 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 12 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 12 weeks ago by
Wolfgang Huber ♦ 13k
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For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
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