Question

Goseq and yeast

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Marek Gierlinski ▴ 30

@mgierlinski-7369

Last seen 12 weeks ago

United Kingdom

We are trying to use goseq on our yeast data, but there is a problem with the yeast database. I managed to create a pwf object with nullp(), but the next step fails:

> pwf = nullp(gene.vector, "sacCer3", "ensGene")
Can't find sacCer3/ensGene length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes. 
> head(pwf)
         DEgenes bias.data        pwf
15S_RRNA       0        NA         NA
21S_RRNA       0        NA         NA
HRA1           0       564 0.04489934
ICR1           0      3199 0.08983848
LSR1           0      1175 0.06094949
NME1           0       340 0.03602508
> GO.wall = goseq(pwf, "sacCer3", "ensGene")
Fetching GO annotations...
Error in toTable(get(paste(orgstring, "GO2ALLEGS", sep = ""))) : 
  error in evaluating the argument 'x' in selecting a method for function 'toTable': Error in get(paste(orgstring, "GO2ALLEGS", sep = "")) : 
  object 'org.Sc.sgdGO2ALLEGS' not found
>

It seems that org.Sc.sgd.db is missing GO2ALLEGS, called by the goseq script. Any suggestions for a fix or workaround?

goseq yeast • 2.0k views

ADD COMMENT • link 9.2 years ago Marek Gierlinski ▴ 30

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Marek Gierlinski ▴ 30

@mgierlinski-7369

Last seen 12 weeks ago

United Kingdom

Thanks, Nadia. This solved the problem!

Cheers,

Marek

ADD COMMENT • link 9.2 years ago Marek Gierlinski ▴ 30

score 3 · Accepted Answer · 2015-02-16

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Nadia Davidson ▴ 310

@nadia-davidson-5739

Last seen 5.0 years ago

Australia

Hi Marek,

It looks like the "GO2ALLEGS" equivalent for yeast is called "GO2ALLORFS". I'll update goseq to fix this, but in the mean time you should be able to manual supply the go mappings like so:

GO.wall=goseq(pwf,gene2cat=as.list(org.Sc.sgdGO2ALLORFS))

Let us know if you still run into any trouble.

Cheers,

Nadia.

ADD COMMENT • link 9.2 years ago Nadia Davidson ▴ 310

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Thanks for the info Nadia, this helped me as well. I have one more question. Is there a fix you know to get the following line to work:

getgo(rownames(topGenes$table), 'sacCer3', 'sgdGene')

I get an error similar to the original post:

object 'org.Sc.sgdGO2ALLEGS' not found

In the end I want to get Iain Gallagher's routine to work (A: goseq analysis - extracting list of my genes which are DE in the enriched GO cat)

ADD REPLY • link 9.0 years ago meono • 0