Creating gene set data for yeast
2
0
Entering edit mode
June. ▴ 10
@june-23879
Last seen 4.3 years ago

Hi,

I want to create gene set for Saccharomyces cerevisiae using go.gsets function from GAGE package. I don't want to use the ready go.sets.sc in the package as I'd like to have the subs info (BP, MF and CC) all together inside the gene set file; this as was also done by developers for human example. But, I get this error:

> go.sc = go.gsets(species = "yeast")
Gene ID type for 'yeast' is: 'ORF'

Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "GO:0000060" not found

Any recommendations for solving this problem?

Thank you!

GAGE gene set go.gsets • 1.5k views
ADD COMMENT
1
Entering edit mode
Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 18 months ago
United States

June, You may want to update your R, BioC and gage/pathview packages to the latest release version. The error should be gone.

You may also install the devel versions from github:
https://github.com/datapplab/gage
https://github.com/datapplab/pathview HTHs,

ADD COMMENT
0
Entering edit mode

Thanks Luo. I updated all, but the problem's still there

ADD REPLY
0
Entering edit mode
Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 18 months ago
United States

please make sure you update the dependencies of gage too, esp. GO.db, AnnotationDbi etc. more info: https://bioconductor.org/packages/gage/
The error you saw is likely due to some recent changes in GO.db etc. The update worked for me when I saw similar problem a few weeks ago.

ADD COMMENT

Login before adding your answer.

Traffic: 622 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6