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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
•
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…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character
by
Kucsera
•
0
After applying your suggestion, the following error pops up:
```
Error in mde(x) : 'list' object cannot be coerced to type 'double'
```
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★
4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do:
`mo…
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