[BioC] biomaRt manual

Weiwei Shi helprhelp at gmail.com
Thu Mar 29 13:02:29 CEST 2007


Sorry :) when I am composing the following email, I did not realize
there are a couple of replies now. I read the manual carefully but I
am still having some questions like this:

For example,

> getBM(attributes=c("affy_hg_u95a", "entrezgene"), filters="affy_hg_u95a", values=head(ids2), mart=human)
  affy_hg_u95a entrezgene
1     31308_at         NA
2     31310_at       2741
3     31312_at       9312
> head(ids2)
[1] "31307_at"   "31308_at"   "31309_r_at" "31310_at"   "31311_at"
[6] "31312_at"
> getBM(attributes=c("affy_hg_u95a", "entrezgene"), filters="affy_hg_u95a", values="31307_at", mart=human)
NULL

I am confused by "NULL" and "NA". I am wondering about the difference b/w them.


Another question is how to make >8000 queries faster though I read
some from previous posts.

Thanks.

Weiwei



On 3/29/07, Weiwei Shi <helprhelp at gmail.com> wrote:
> Thanks, Kasper. But I did use method B and found the vignettes.
> However, it seems that one is not written in very detailed.
>
>
>
> On 3/29/07, Kasper Daniel Hansen <khansen at stat.berkeley.edu> wrote:
> > As most Bioconductor packages, biomaRt comes with a vignette
> > (actually 2). Read it :)
> >
> > To do so, you can do one of several steps
> >
> > Method a)
> > R> vignette()
> > will give you a list of vignettes on your system, alternatively you
> > can try
> > R> vignette(package = "biomaRt")
> > Doing
> > R> vignette("NAME")
> > will open one.
> >
> > Method b)
> > Use Biobase vignette browser:
> > R> library(Biobase)
> > R> openVignette()
> > This differs from vignette in
> > * Only vignettes from loaded packages are shown (so you need to do R>
> > library(biomaRt) first)
> > * You get a selection menu
> >
> > Method c)
> > Download it from the package webpage on www.bioconductor.org
> >
> > Kasper
> >
> > On Mar 28, 2007, at 9:06 PM, Weiwei Shi wrote:
> >
> > > Hi,
> > > I have a simple question on using biomaRt but I did not find a proper
> > > manual to follow.
> > >
> > > I have a list of probes with affy ids and I want to convert them into
> > > entrezgene id. Is there a manual or example I can follow?
> > >
> > > Thanks.
> > >
> > > --
> > > Weiwei Shi, Ph.D
> > > Research Scientist
> > > GeneGO, Inc.
> > >
> > > "Did you always know?"
> > > "No, I did not. But I believed..."
> > > ---Matrix III
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives: http://news.gmane.org/
> > > gmane.science.biology.informatics.conductor
> >
> >
>
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III



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