User: christopherlhartl

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Posts by christopherlhartl

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DESeq2 - lfcShrink reversing sign for all logFCs - clarification on "contrast" argument?
... Hi there, I've got a little snippet that merges raw (non-shrunk) log-FC values with shrinkage values ``` model.str <- "~ genotype + individual" eset$genotype <- factor(eset$genotype, levels=c('WT', 'KO')) eset.model <- DESeqDataSet(eset, design=formula(model.str)) eset.fit = DESeq(eset.mo ...
deseq2 written 4 days ago by christopherlhartl0 • updated 4 days ago by Michael Love25k
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Answer: A: Cannot install Bioconductor v3.9
... This is an issue with the CA certificate of bioconductor.org expiring; and the fact that bioconductor does not use an http fallback for https. In the meantime you can perform a manual installation, using the base R install.packages, and specifying the bioconductor repo directly, as in: instal ...
written 18 days ago by christopherlhartl0 • updated 18 days ago by Martin Morgan ♦♦ 23k
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Comment: C: GO.db installation error
... Just to answer my question: this is a filesystem issue.    > .libPaths('/tmp') > biocLite('GO.db') ** testing if installed package can be loaded * DONE (GO.db)   So a workaround if you're on such a filesystem: put the source .tar.gz in a central location, and you'll need to freshly instal ...
written 3.4 years ago by christopherlhartl0 • updated 3.4 years ago by Martin Morgan ♦♦ 23k
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Comment: C: GO.db installation error
... Just hit this myself with a fresh install (from source) of R:   R version 3.3.0 (2016-05-03) -- "Supposedly Educational" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > source('http://bioconductor.org/biocLite.R') Bioconductor version 3.3 ...
written 3.4 years ago by christopherlhartl0 • updated 3.4 years ago by Martin Morgan ♦♦ 23k

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