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Answer: How do I fix an odd voom plot in a combined dataset?
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Gordon Smyth
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voom is a DE analysis method rather than a normalization method. voom expects the design matrix to be the same complete design matrix that …
Comment: enrichGOgradient color change
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lewis.roper
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I know you submitted this months ago but you're an absolute lifesaver mate, thank you
Comment: Warning message when running limma with covariates
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Chris
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Hi @gordonsmyth. Happy New Year! Wishing you all the best in 2025. Thank you so much for your kind support!
Comment: minfi latest update for EPIC V2 chip
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macdonaldfrench7286566
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0
Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo.
*Th…
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
To compute CPM values from edgeR:
```
y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status)
y <- …
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