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Comment: deseq2 filter the low counts by goldenboy • 0
Dear Michael, following this code: library(tidyverse) library(tximportData) library(tximport) library(tximeta) library…
Comment: Suggested package missing from Development version of Bioconductor by Richard • 0
I have just contacted the maintainer. Is it okay if I leave the package in Suggests for now and then remove it before the next Bioconductor…
Answer: shinyMethyl - saving the file by Guillaume Devailly ▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
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DESeq2 analysis with only two replicates
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
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