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MBD-seq non model species
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Comment: DESeq2 false positive result?
The average of U2 is different in a than it is in b. You can't expect DESeq to automatically remove outliers, if you judge that those two …
Answer: GDCprepare : Error: BiocParallel errors/Error in stopAndCache(title):
Make sure you have installed the sesame library first. then run sesameDataCache(). Catching need to be done only once per installation.
Answer: Changing the sample order in the PCA plot
You have to change the factor levels in the vsd object itself, so `vsd$condition <- factor(as.character(vsd$condition), levels=c("day0", "…
Comment: ASICS - Include internal standard in analysis
Hi Chris, Unfortunately I have not find any solution to the problem. I tried to change the ppmgrid, making it start at -0.5ppm and includi…
Comment: normalization of ChIP-seq data by using the spike-ins or by using total library
On another topic, talking about edgeR or limma, any thoughts regarding the computation of the normalization factors as Gordon Smith sugges…
Answer: problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignmen
problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0
DESeq2 false positive result?
What was the very first paper to describe "limma-trend"?
How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
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