Dear BioC users,
I am having the following data,
background.Datat: Entrez identifiers of all probes present on Illumina
human HT12 v3. microarray
DEgenes.Data: Differentially expressed genes in a real study carried
out on Illumina HT12 v3. microarray
Can anyone suggest, how to construct GOgraph for the available
data....Thanks in advance.
Regards,
Pradee.
On Mon, Nov 8, 2010 at 5:41 PM, Pradeep Battula <prabat@utu.fi> wrote:
> Dear BioC users,
>
> I am having the following data,
>
> background.Datat: Entrez identifiers of all probes present on
Illumina
> human HT12 v3. microarray
> DEgenes.Data: Differentially expressed genes in a real study carried
out on
> Illumina HT12 v3. microarray
>
> Can anyone suggest, how to construct GOgraph for the available
> data....Thanks in advance.
>
>
Hi, Pradeep.
You will probably want to do a hypergeometric testing procedure to
find the
enrichment of your genes in various GO categories. I think Steve
emailed
you how to do that a couple of days ago using the GOstats package.
There is
an mailing list archive (link attached to every email) available if
you
missed that email. If Steve's suggestion doesn't work for you, please
send
the code you tried, errors you received, and the output of
sessionInfo().
As for making a GO graph, you may want to take a look at the help for
GOgraph() in the GOstats package. Again, if you get an error, please
supply
a reproducible example and the output of sessionInfo().
Sean
[[alternative HTML version deleted]]
Hi, Sean.
The information provided by Steve helped me a lot in carrying out the
GO enrichment tests. But now, I want to visualize the results in the
GO graph. Regarding that I need suggestions.....Thank You.
Regards,
Pradeep.
----- Original Message -----
From: Sean Davis <sdavis2@mail.nih.gov>
Date: Tuesday, November 9, 2010 1:03 am
Subject: Re: [BioC] Need suggestions for constructing GOgraph
To: Pradeep Battula <prabat at="" utu.fi="">
Cc: bioconductor at stat.math.ethz.ch
> On Mon, Nov 8, 2010 at 5:41 PM, Pradeep Battula <prabat at="" utu.fi="">
wrote:
>
> > Dear BioC users,
> >
> > I am having the following data,
> >
> > background.Datat: Entrez identifiers of all probes present on
Illumina
> > human HT12 v3. microarray
> > DEgenes.Data: Differentially expressed genes in a real study
carried
> out on
> > Illumina HT12 v3. microarray
> >
> > Can anyone suggest, how to construct GOgraph for the available
> > data....Thanks in advance.
> >
> >
> Hi, Pradeep.
>
> You will probably want to do a hypergeometric testing procedure to
> find the
> enrichment of your genes in various GO categories. I think Steve
emailed
> you how to do that a couple of days ago using the GOstats package.
> There is
> an mailing list archive (link attached to every email) available if
you
> missed that email. If Steve's suggestion doesn't work for you,
please
> send
> the code you tried, errors you received, and the output of
sessionInfo().
>
> As for making a GO graph, you may want to take a look at the help
for
> GOgraph() in the GOstats package. Again, if you get an error,
please
> supply
> a reproducible example and the output of sessionInfo().
>
> Sean
On Mon, Nov 8, 2010 at 6:19 PM, Pradeep Battula <prabat@utu.fi> wrote:
> Hi, Sean.
>
> The information provided by Steve helped me a lot in carrying out
the GO
> enrichment tests. But now, I want to visualize the results in the GO
graph.
> Regarding that I need suggestions.....Thank You.
>
>
Hi, Pradeep.
Sorry to be so difficult, but we cannot help you unless you try things
yourself. Please read the help for GOgraph in the GOstats package.
If you
have problems, please send the code you tried and the error messages
you
receive.
Sean
> Regards,
> Pradeep.
>
> ----- Original Message -----
> From: Sean Davis <sdavis2@mail.nih.gov>
> Date: Tuesday, November 9, 2010 1:03 am
> Subject: Re: [BioC] Need suggestions for constructing GOgraph
> To: Pradeep Battula <prabat@utu.fi>
> Cc: bioconductor@stat.math.ethz.ch
>
>
> > On Mon, Nov 8, 2010 at 5:41 PM, Pradeep Battula <prabat@utu.fi>
wrote:
> >
> > > Dear BioC users,
> > >
> > > I am having the following data,
> > >
> > > background.Datat: Entrez identifiers of all probes present on
Illumina
> > > human HT12 v3. microarray
> > > DEgenes.Data: Differentially expressed genes in a real study
carried
> > out on
> > > Illumina HT12 v3. microarray
> > >
> > > Can anyone suggest, how to construct GOgraph for the available
> > > data....Thanks in advance.
> > >
> > >
> > Hi, Pradeep.
> >
> > You will probably want to do a hypergeometric testing procedure to
> > find the
> > enrichment of your genes in various GO categories. I think Steve
emailed
> > you how to do that a couple of days ago using the GOstats package.
> > There is
> > an mailing list archive (link attached to every email) available
if you
> > missed that email. If Steve's suggestion doesn't work for you,
please
> > send
> > the code you tried, errors you received, and the output of
sessionInfo().
> >
> > As for making a GO graph, you may want to take a look at the help
for
> > GOgraph() in the GOstats package. Again, if you get an error,
please
> > supply
> > a reproducible example and the output of sessionInfo().
> >
> > Sean
>
[[alternative HTML version deleted]]
