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List:       bioc-devel
Subject:    Re: [Bioc-devel] ath1121501 hyperGTest
From:       Marc Carlson <mcarlson () fhcrc ! org>
Date:       2009-05-06 22:40:47
Message-ID: 4A0211EF.7010707 () fhcrc ! org
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Hi Kaiyu,

You want to share your sessionInfo() with us when you post.  That will
make it much easier for us to know how to reproduce any troubles you
might have.  Assuming that you are using the latest stuff (and you
should be since you are using an annotation package), then you are
correct about needing to use the identifiers in the ACCNUM mapping. 
These IDs are gene IDs from TAIR, and they are the central gene ID used
by our arabidopsis gene databases. 

I am not sure why you are trying to copy the ath1121501ACCNUM mapping
onto the ath1121501ENTREZID mapping but I am pretty sure this won't
help.  What you should probably be doing instead is defining a gene
universe and a list of interesting genes that are represented "as" TAIR
IDs.  You can use the ath1121501ACCNUM mapping to help you do this.  If
the geneIds and universeGeneIds parameters are not vectors of TAIR IDs,
then this process is just not going to work so be sure to makes sure
that these things are set up correctly.  To see a more complete set of
instructions for using GOstats to do hypergeometric testing you might
want to look at the package vignette on this topic:

http://www.bioconductor.org/packages/release/bioc/html/GOstats.html

And here is a toy example for arabidopsis for you to look at:


library(GOstats)
library(ath1121501.db)

##fake some IDs to just fill out the parameters
universe = mappedRkeys(ath1121501ACCNUM);
##"interesting" here is defined to be the 1st 400 in the "universe"
IDs = universe[1:400]

params <- new("GOHyperGParams", geneIds = IDs,
universeGeneIds = universe, annotation = "ath1121501",
ontology="BP", pvalueCutoff=0.05, conditional=FALSE,              
testDirection = "over")

Over <- hyperGTest(params)
Over
summary(Over)



  Marc





Kaiyu Shen wrote:
> Hi, folks:
> I am now dealing with the ath1121501.db package and the hyperGTest in
> GOStats. 
> I have pulled out a list of genes, with their probe ID.
> these genes are selected with their GO term available, and no
> duplicates.
> I tried:
> params=new("GOHyperGParams",geneIds=gene.list,annotation="ath1121501",ontology="BP",
> pvalueCutoff=0.05, conditional=FALSE,testDirection="over")
> result=hyperGTest(params)
>
> However,they give me an error message :
>
> Error in get(mapName, Envir=pkgEnv,inherits=FALSE):
> variable "ath1121501ENTREZID" was not found
> Error in mget(probes,ID2EntrezID(datPkg)):
> error in evaluating the argument 'envir' in selecting a method for
> function 'mget'
>
> I searched online, and found that someone said in ath1121501.db, the
> ENTREZID equals to the ACCNUM,so I tried to directly assign the value
> as:
> ath1121501ENTREZID<-ath1121501ACCNUM
>
> however, error message still pops out. 
> Does anybody have a clue of how this could be solved??
>
> Thanks again. 
> Kyle.
>
> _______________________________________________
> Bioc-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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