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Comment: Warning message when running limma with covariates
by
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
by
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 <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets
by
Gordon Smyth
52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets
by
Andre
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0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
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