User: johnmcma

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johnmcma10
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Posts by johnmcma

<prev • 14 results • page 1 of 2 • next >
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"Mixed" in romer output
... Hi, The output of `romer` in `limma` includes a field called "Mixed." The man page defines it as "[...]p-values for the alternative hypotheses mixed[...]", but neither paper cited mention what that alternate hypothesis actually means. Can anyone enlighten me as to what that p-value actually means? ...
limma romer written 4 months ago by johnmcma10 • updated 4 months ago by James W. MacDonald46k
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Comment: C: Comparing Expression Ratios between two genes
... Noted. Is it, however, acceptable to use the same weights as generated by voom on the original transcriptome? ...
written 5 months ago by johnmcma10
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Comment: C: Comparing Expression Ratios between two genes
... Hi Dr Smyth, the data involved are RNA-seq data. John ...
written 5 months ago by johnmcma10
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Comparing Expression Ratios between two genes
... Hi board, We are currently interested in using limma to identify whether the ratios between the expression of two genes are different between two groups of individuals. Is it sound to generate an extra row of Exp(A)/Exp(B) on the expression matrix and progress with the usual limma pathway, or shoul ...
limma written 5 months ago by johnmcma10 • updated 5 months ago by Gordon Smyth34k
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Answer: A: DESeq2, no replicate
... DESeq(2) and edgeR are not intended to be used with designs with less than 3 replicates. For those designs, NOIseq or GFOLD may be better choices, but it's still not a good idea to draw conclusions based on their results. ...
written 9 months ago by johnmcma10
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Illumina array weights--arrayWeights or beadCountWeights
... I have several sets of Illumina data that assigning quality weights is appropriate for a limma analysis. While `arrayWeights` is very frequently used, I have noticed limma has the function `beadCountWeights` that appears to be performing quality weighting for BeadChips, but that function was never d ...
limma arrayweights written 9 months ago by johnmcma10 • updated 9 months ago by Gordon Smyth34k
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Optimizing the deepSplit parameter in dynamicTreeCut
... I'm planning to write code to optimize the `deepSplit` parameter in dynamicTreeCut in a way not unlike what's already been doing in `clValid`, which uses common cluster validity indexes to optimize k for `cutree`. The problem is: dynamicTreeCut occasionally decides some genes as unclustable (i.e. c ...
dynamictreecut written 13 months ago by johnmcma10
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Limma: difference between groups of paired data
... So let us assume in addition to the setup in Part 9.4.1 of the User Guide, I'm also adding a variable called Schedule, referring to two types of scheduling for the tested treatment. So the targets frame would look like this: FileName SibShip Treatment Schedule File1 ...
limma limma paired analysis written 14 months ago by johnmcma10 • updated 14 months ago by Aaron Lun20k
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Comment: C: Using DESeq2 with Nanostring data (for VST only)
... The number of probesets is not an issue; this project involves more than one complete set (of 768 "Endogenous" probes). ...
written 15 months ago by johnmcma10
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Comment: C: Using DESeq2 with Nanostring data (for VST only)
... By "normalized" I solely mean Nanostring's own CodeSet normalization. But should I put in the positive controls only, or also the negative controls as well? From what I know, Nanostring's own guidelines no longer recommends performing background deductions. ...
written 15 months ago by johnmcma10

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Popular Question 13 months ago, created a question with more than 1,000 views. For Is there any point to TMM-normalize TPM prior to limma-voom?

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