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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
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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:
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# estimate d…
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It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
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Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
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Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
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pheno <- rnb.set.arrays@pheno # Phenotypic data
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