User: johnmcma

johnmcma10
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Posts by johnmcma

<prev • 14 results • page 1 of 2 • next >
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... 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? ...
written 14 months ago by johnmcma10 • updated 14 months ago by James W. MacDonald50k
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280
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... Noted. Is it, however, acceptable to use the same weights as generated by voom on the original transcriptome? ...
written 15 months ago by johnmcma10
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280
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... Hi Dr Smyth, the data involved are RNA-seq data. John ...
written 15 months ago by johnmcma10
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280
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... 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 ...
written 15 months ago by johnmcma10 • updated 15 months ago by Gordon Smyth37k
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... 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 19 months ago by johnmcma10
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300
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... 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 ...
written 19 months ago by johnmcma10 • updated 19 months ago by Gordon Smyth37k
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288
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... 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 ...
written 23 months ago by johnmcma10
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675
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... 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 ...
written 2.0 years ago by johnmcma10 • updated 2.0 years ago by Aaron Lun23k
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... The number of probesets is not an issue; this project involves more than one complete set (of 768 "Endogenous" probes). ...
written 2.1 years ago by johnmcma10
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... 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 2.1 years ago by johnmcma10

Latest awards to johnmcma

Popular Question 4 months ago, created a question with more than 1,000 views. For Using DESeq2 with Nanostring data (for VST only)
Popular Question 23 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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