User: Will Landau

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Posts by Will Landau

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Comment: C: biocLite on R 3.2.0 stalls then vanishes
... That worked, so I guess I'm unstuck. Thanks. I'm still wondering why rerunning source("http://bioconductor.org/biocLite.R") was necessary, though. Also, biocLite didn't initially pay attention to my .libPaths() (set in .Rprofile): > .libPaths() [1] "/home/landau/.R/library" "/apps/R-3.2.0/lib ...
written 4.6 years ago by Will Landau0
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biocLite on R 3.2.0 stalls then vanishes
... I just upgraded to R 3.2.0, stashed all my old packages, and got ready to reinstall all my Bioconductor packages. I tried to run biocLite(), but the function just paused indefinitely. When I hit CTRL-C and tried again, R couldn't find biocLite anymore. Here's the whole session.   R version 3.2.0 ( ...
bioclite software error written 4.6 years ago by Will Landau0 • updated 4.6 years ago by Dan Tenenbaum8.2k
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Comment: C: Use DESeq2 to test if hybrid > max(parent1, parent2) | hybrid < min(parent1, par
... I have no idea how that argument got there, I didn't mean to set lfcThreshold at all. Removing it seems to remove or mask the problem in that example. Thank you! ...
written 4.6 years ago by Will Landau0
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Use DESeq2 to test if hybrid > max(parent1, parent2) | hybrid < min(parent1, parent2)
... I'm trying to use DESeq2 to test if hybrid > max(parent1, parent2) | hybrid < min(parent1, parent2), where parent1, parent2, and hybrid are three genetic varieties. The DESeq2 framework doesn't directly do this kind of hypothesis test, so I test a bunch of contrasts and then pick the p-value f ...
deseq2 written 4.6 years ago by Will Landau0
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Comment: C: more complicated hypotheses than differential expression (with baySeq or a simil
... Thanks, that sounds reasonable.  ...
written 5.1 years ago by Will Landau0
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more complicated hypotheses than differential expression (with baySeq or a similar package)
... I have an RNA-seq dataset with 3 treatment groups, where gene g has group means mu_{g, i} for i = 1, 2, 3. Is there a way to use baySeq to calculate the posterior probabilities that mu_{g, 2} > max(mu_{g, 1}, mu_{g, 3}) and the posterior probabilities that  mu_{g, 2} < min(mu_{g, 1}, mu_{g, 3} ...
bayseq hypotheses written 5.1 years ago by Will Landau0 • updated 5.1 years ago by Gordon Smyth39k

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