Question: Error in biomaRt using phytozome_mart
0
gravatar for nick.lorusso
6 months ago by
nick.lorusso0 wrote:

I am trying to download information from JGI phytozome for a differential expression analysis I ran using DESeq2. A wealth of googling hasn't yielded anything that fixes the issue.

I'm trying to troubleshoot what I'm doing wrong so I have some test code below:

vol = useMart(biomart = "phytozome_mart", host="phytozome.jgi.doe.gov", dataset = "phytozome")

IDS = c("Cre01.g000017.t1.1","Cre01.g000033.t1.1","Cre01.g000650.t1.1")
check = getBM(attributes=c("transcript_name1","gene_name"),
                  filters = "transcript_name_filter", 
                  values = IDS, 
                  mart = phytozome_mart)

Running this gives me a consistent error of:

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: NA

Which I'm not sure how to resolve. I can successfully use listAttributes and listMarts on vol to see the information from phytozome, but I don't know why I get an error when trying to access them.

Any help would be appreciated. I've used biomaRt successfully in the past to pull information from other marts, so I'm not sure what's going wrong this time...

rna-seq R • 228 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by nick.lorusso0
2

Please try the recent answer relating to the same topic: Retrieving phytozome data using the R bioconductor package biomaRt

ADD REPLYlink written 6 months ago by Kevin Blighe26k

...darn it.

I had seen that post, tried to implement it (as part of the 4 other solutions I found), and wrote it off when it didn't work. I had an issue with my input table...

Thanks for taking the time, at the very least you pointed me back to the best solution.

ADD REPLYlink written 6 months ago by nick.lorusso0

Okay, so, it's fine now, right?

ADD REPLYlink written 6 months ago by Kevin Blighe26k
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