User: jbatsx

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Posts by jbatsx

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Limma fixed and random effects
... I have read around and cannot find a similar example to this particular case and I'm still not clear so I apologise if this is a trivial question. I have data for an experiment which consisted of two diseases and a control group. The disease groups (C1, C2) consists of those which have been treated ...
limma written 2.3 years ago by jbatsx0 • updated 2.3 years ago by Gordon Smyth37k
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Comment: C: DESeq2 16s microbiome size factors
... I did apply metagenomeSeq, but it gave me gave me a lot more differentially abundant OTUs than wilcoxon tests or DESeq2 . DESeq/Wilcoxon tests (on TMM normalised counts) give me ~ 50 species whereas metagenomeSeq finds 140. I'm only looking at the 300 most abundant so finding half of these to be sig ...
written 2.6 years ago by jbatsx0
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Comment: C: DESeq2 16s microbiome size factors
... Thanks Micheal, I tired calculating the the size factors using the upper quantile method, I found a code snippet mentioned in another thread: qs <- apply(counts(dds), 2, quantile, .90) sf <- qs / exp(mean(log(qs))) sizeFactors(dds) <- sf Around 20 samples are 0 at the 0.90 quantile, I ...
written 2.6 years ago by jbatsx0
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DESeq2 16s microbiome size factors
... Hi, I am trying to use DESeq2 to perform differential analysis on a large 16s microbiome dataset of around 600 samples. It is clear from our current non-parametric analysis that many of our OTUs of interest are associated with one or more unwanted covariates. We want to use a parametric model like ...
rnaseq microbiome deseq2 metagenomeseq 16s written 2.6 years ago by jbatsx0 • updated 2.6 years ago by Joseph Nathaniel Paulson270

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