User: johnmcma

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johnmcma10
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Posts by johnmcma

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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 18 days 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 21 days ago by johnmcma10 • updated 19 days ago by Gordon Smyth32k
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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 4 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 5 months ago by johnmcma10 • updated 5 months ago by Aaron Lun16k
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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 6 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 6 months ago by johnmcma10
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Comment: C: Using DESeq2 with Nanostring data (for VST only)
... What if I just don't put in the spike-ins? And, from what you mentioned above, I guess you refer to nCounts that have not been normalized, right? ...
written 6 months ago by johnmcma10
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Using DESeq2 with Nanostring data (for VST only)
... Hi all, Right now I'm planning to perform some machine learning analyses on Nanostring data, and would like to experiment coercing the data to linear by DESeq2's VST functions, as VST has been working fine with out RNA-seq data. However, unlike limma-voom, there're few guidance for using DESeq(2) ...
deseq2 variancestabilizingtransformation nanostring written 6 months ago by johnmcma10 • updated 6 months ago by Michael Love14k
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Comment: C: Is there any point to TMM-normalize TPM prior to limma-voom?
... Well, by triggering the argument countsFromAbundance, the counts slot of the tximport output is derived using the abundance measure named in the command (by default, TPM for the fishes and FPKM for RSEM). I'm citing the code in question below: makeCountsFromAbundance <- function(countsMat, abun ...
written 6 months ago by johnmcma10
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Is there any point to TMM-normalize TPM prior to limma-voom?
... The current tximport vignette recommends the following workflow for limma-voom input: files <- file.path(dir, "kallisto", samples$run, "abundance.tsv") names(files) <- paste0("sample", 1:6) txi <- tximport(files, type = "kallisto", tx2gene = tx2gene, reader = read_tsv,     countsFromAbun ...
edger voom tximport limma-voom written 6 months ago by johnmcma10 • updated 6 months ago by Ryan C. Thompson6.1k

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