Devarajan, Karthik wrote:
> Hello,
>
> I'm trying to apply enrichment analyses to gene lists obtained from
> yeast data using GOstats. I want to use the Yeast GO slim annotation
to
> do the analysis. My yeast data is from the SGD database and it is
not
> clear to me which annotation package I should use. The package
> org.Sc.sgd.db is not supported yet and the YEAST package does not
seem
> to contain the required probe names. Does anyone have any idea what
> FIXME (mentioned in the Bioconductor help file for YEAST) refers to?
I'd
> appreciate any input regarding this issue.
>
> Thanks,
> K
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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Hi Karthik,
I would like to try and help you but I need a lot more information.
What is your sessionInfo()? And what specifically is not supported
that
you want to do? In general I recommend for people to use the newer
org.Sc.sgd.db packages for organism based annotations. These packages
should emulate all the same functionality as the older annotations
packages that they are replacing (in this case YEAST is being replaced
by org.Sc.sgd.db).
Marc
Hi Karthik,
Can I further ask what you are using for gene identifiers here? If
you
are using something other than yeast systematic names, then I suspect
you will have trouble. These are the yeast IDs that look like:
"YAL001C", or "YGR116W".
On a related note, I will correct the error you found in the vignette
so
that it will state that you are supposed to use yeast systematic names
with the YEAST package.
Does this help?
Marc
Devarajan, Karthik wrote:
> Hi Mark,
>
> I was using the gene identifiers from the SGD - they look like
S000001,
> S000002 etc. I have now been able to map these to corresponding
yeast
> ids and it's working!
>
> Thanks very much for your help with this.
>
> Do you know when org.Sc.sgd.db will be supported?
>
> Best,
> Karthik
>
Hi Karthik,
I am glad to hear that you found out what the problem was and that
everything is working now.
As for your question about the org.Sc.sgd.db, I can't know for sure
because you never posted enough of an example for me to replicate
everything that you were doing. But in the email you sent to me
before
you had this:
> params <- new("GOHyperGParams", geneIds=gene.id,
universeGeneIds=gene.all, annotation="org.SC.sgd.db", ontology="CC",
pvalueCutoff=hgCutoff,conditional=FALSE, testDirection="over")
> hgOver <- hyperGTest(params)
Error: getAnnMap: package org.SC.sgd not available
And THAT will definitely not work just because the actual package is
called "org.Sc.sgd.db" and not "org.SC.sgd.db"... The "org.Sc.sgd.db"
package should have everything in it that you would find in the
"YEAST"
package. So I would be surprised if that package does not work for
you
here as well.
Marc
