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Comment: Identifying potentially associated gene set to drug response using GSVA
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coolmathforkids2
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It is always helpful to see clear explanations and solutions for bioconductor related challenges. Posts like this make the community a valu…
Comment: minfi latest update for EPIC V2 chip
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macdonaldfrench7286566
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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
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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
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Andre
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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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