Hi Marc,
The code is working.
I will have to include in the code to extract the IPI's in my list.
Thanks,
Viritha



On Wed, Mar 9, 2011 at 8:30 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Viritha,
>
> The merge function is in base R.
>
> What is the output from your sessionInfo()
>
>
>  Marc
>
>
> On 03/09/2011 01:19 PM, viritha kaza wrote:
> > Hi Marc,
> > Thanks for the explanation.I now realised that there can not be 1:1
> > relation between the IPI and the Entrez ids. Like how Dick was saying
> > I used both the methods first by the site:
> > ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.xrefs.gz.
> > and then the remaining with the code in biomart:
> > as I had mentioned previously
> >  code:
> > >source('http://bioconductor.org/biocLite.R')
> > > biocLite("biomaRt")
> > >library("biomaRt")
> >  >ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > >ipi=scan("ipi_test.txt",what =character(),sep='\n',quote="")
> > # ipi_test file contained the IPI's that I wanted to convert
> > >getBM(attributes =
> > c("ipi","entrezgene","hgnc_symbol"),filters="ipi",values=ipi,mart =
> > ensembl)
> > >write.table(ipi_entrez,"ipi_entrez_test.txt",sep='\t')
> >
> > I could not find the merge method of yours which dick was mentioning.
> > For now I am only interested in the entrez id and genesymbol only for
> > the respective IPI in my list.
> > Is there an easy method for this and if they could share it, then it
> > would be excellent.
> > Thanks,
> > Viritha
>
>

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