Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... 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.
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written 26 days ago by
Wolfgang Huber ♦ 13k
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... 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 Huber ♦ 13k
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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 3 months 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 4 months 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 4 months 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 4 months 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 4 months 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 months 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 months ago by
Wolfgang Huber ♦ 13k
0
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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.
...
written 4 months 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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For A: package specifically dedicated to a manuscript
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