User: johnmcma

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Posts by johnmcma

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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 11 days ago by johnmcma0 • updated 11 days ago by Aaron Lun14k
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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 5 weeks ago by johnmcma0
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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 5 weeks ago by johnmcma0
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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 weeks ago by johnmcma0
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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 weeks ago by johnmcma0 • updated 6 weeks ago by Michael Love12k
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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 7 weeks ago by johnmcma0
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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 7 weeks ago by johnmcma0 • updated 7 weeks ago by Ryan C. Thompson5.7k

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