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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
•
0
They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find:
````
# estimate d…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
•
0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species
by
Jeremy
•
0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error?
by
Urotree
•
0
pheno <- rnb.set.arrays@pheno # Phenotypic data
sites <- rnb.set.arrays@sites # CpG site definitions (data.frame)
meth <- rnb.set…
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