updated 10 months ago by
b.signal
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written 11 months ago by
frank.maiwald
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Comment: pathview says my nonmodel species is unknown: "species invalid"
by
James W. MacDonald
60k
Ah, I get it. So what happens if you provide a species code (which can be an actual species code or the genus and species or even a common …
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
nute11a
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0
Hi James, thanks so much for your response! I actually did:
```
test <- pathview(gene.data=geneList, pathway.id="00440", species="ppyr")
``…
Comment: DESeq2 on normalized data
by
ATpoint
★
1.4k
It’s not supported. Use limma-trend with the log2-transformed normalized counts if that is all you have. See limma manual.
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
James W. MacDonald
60k
My answer was a bit of a word salad, so perhaps this will illustrate better what I meant.
```
## create a character object
> MyKEGGSpecies…
Answer: pathview says my nonmodel species is unknown: "species invalid"
by
James W. MacDonald
60k
If you have a character object called 'MySpeciesCode' that is just your species code, then you have to pass that object to the function, **…
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