[BioC] GOTERM by itself

[Saurin Jani]

Hi Sean,

I got it upto:

myLL <- getLL(myDEGenes,"moe430a");
myUNQLL  <-
as.character(na.omit(unique(unlist(myLL))));

myGOHyp <-  GOHyperG(myUNQLL);

myGOCC <-  GOHyperG(myUNQLL, lib="moe430a",
what="CC");
DECCnodes = names(myGOCC$intCounts);
CCTERMS <- getGOTerm(DECCnodes);
DECCnodes2affy = lookUp(DECCnodes,GO2ALLPROBES);

unlist and paste is not working on DECCnodes2affy
object as it has:

$"GO:0005663"
           IEA            IEA            IEA          
 ISS            ISS
  "1418342_at"   "1449050_at" "1451920_a_at"  
"1417503_at"   "1423700_at"
           ISS            IEA            ISS
"1432538_a_at"   "1452917_at"   "1424321_at



now , how can I count each probe ids under GOID in
List object.

Could you please help me ?

Thank you,
Saurin


--- Sean Davis <sdavis2 at mail.nih.gov> wrote:

> 
> On Oct 14, 2004, at 10:21 AM, Saurin Jani wrote:
> 
> > Hi Auer,
> >
> > I would like to do similar thing with GOTERM as
> you
> > are doing at some extent but I would like to build
> > table like :         (I am using Affy chips here)
> >
> > GOTERM ,count of ProbeIDS associated with them ,
> > ProbeIDS itself , SYMBOLS of probe ids
> >
> > any idea on this ?
> >
> > Thanks
> > Saurin
> 
> Saurin,
> 
> You can get the probeids associated with a GO term
> from the GO2PROBES 
> or GO2ALLPROBES environments using lookUp.  You can
> get the symbols of 
> those probes using getSYMBOL.  A judicious use of
> unlist and paste, 
> combined in a final data.frame should do the trick.
> 
> Sean
> 
>