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Answer: List of DEGs belonging to an Agilent-single color microarray experiment using Li by Gordon Smyth 51k
The first coefficient in your linear model appears to be an intercept term. In this context, you should not be using `method="global"` beca…
Comment: Package needs internet access by firestar ▴ 20
Updated with more code.
Comment: Package needs internet access by James W. MacDonald 67k
It's not clear to me why (or that) `seqlevelsStyle` should be called on a `BSgenome` object. You will need to provide more code that preced…
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela by James W. MacDonald 67k
The 'voom transformed counts' are just logCPM with a prior count of 0.5. The 'magic' of limma-voom is the weights that are computed and the…
Comment: Limma Interaction Effect with Covariates by kitzhu • 0
Thanks so much, James!
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Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Comment: Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
Dotplot from enricher outputting very few genes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
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