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Comment: DESeq 2 failes to load
by
Ruggero
•
0
This solved the error, in case someone else is having compilation errors from installing RSQllite:
install.packages('RSQLite', repos='http…
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
Guido Hooiveld
★
3.3k
A while ago a faced the same for another non-model organism. I was able to get it working using a 'hack'. This hack is nothing more than ma…
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
•
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.
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