Creating gene set data for yeast
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June. ▴ 10
@june-23879
Last seen 14 months 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 • 345 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 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,

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

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 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.

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