Open matthewabirk opened 5 years ago
Hi @matthewabirk:
I have not yet enabled more complex designs within elvers
. I'd recommend you grab the .deseq2.rds
(R data) file from the deseq2
output directory, and work with deseq2
directly in R
.
You can see elvers/elvers/rules/deseq2/deseq2-init-tx2gene.R
or elvers/elvers/rules/deseq2/deseq2-init-txOut.R
for how this dataset is being generated from the salmon counts.
https://support.bioconductor.org/p/102445/ might also be helpful.
Thanks! Just a note: the last two lines of deseq2.R
are currently:
write.table(as.data.frame(res), file=snakemake@output[["table"]])
write.table(as.data.frame(res), file=snakemake@output[["sigTable"]])
Shouldn't the 2nd line be?
write.table(as.data.frame(sigRes), file=snakemake@output[["sigTable"]])
fixed - thanks!
I can't figure out how to configure my yaml to allow DESeq2 to test 3 treatments.
When I try
Then, I get an error in
/automounts/workspace/workspace/mbirk/artemia/artemia_out_all/logs/deseq2/artemia_input.csalinity.deseq2.log
:I also tried:
But then the only output is the last set of contrasts. What's the proper way to format the yaml for this?