[BioC] GOstats: another problem

[James MacDonald]

Simon,

The reason you are not getting the correct result is because of typos.

You did:
get("GO:0003700", OFFSPRING)

Jianhua did:
get("GO:0003700", GOMFOFFSPRING)
                  ^^^

In addition, there is no such thing as GOMFOFFSPRINGS, which is why that
environment was not found.


HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Simon Lin" <simon.lin at duke.edu> 07/30/04 6:47 PM >>>
John:

One more question to bother you. I have GO_1.5.1 installed.

But GOMFOFFSPRINGS is not part of the environment variable; neither is
GOLOCUSID.

See below:

> get("GO:0003700", OFFSPRING)
Error in get("GO:0003700", OFFSPRING) :
        Object "OFFSPRING" not found

> GO
<environment: 020372E8>

> GOMFOFFSPRINGS
Error: Object "GOMFOFFSPRINGS" not found

> GOMFCHILDREN
<environment: 02E1ADF0>

> GOLOCUSID
Error: Object "GOLOCUSID" not found
>

Any suggestions?

Thanks!

Simon


----- Original Message ----- 
From: "John Zhang" <jzhang at jimmy.harvard.edu>
To: <simon.lin at duke.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Friday, July 30, 2004 2:57 PM
Subject: Re: [BioC] GOstats:


>
> >How to find all the off-springs (not only direct children) of a GO
term,
say
> >"GO:0003700"?
>
> >library(GO)
> >get("GO:0003700", GOMFOFFSPRING)
> [[1]]
> [1] "GO:0003705"
>
>
> >And how to find all the LocusLink IDs associated with these GO terms?
> >Take these two questions together, I want to find all the LL-IDs
associated
> >with a GO node at certain level.
>
> > mget(unlist(get("GO:0003700", GOMFOFFSPRING)), GOLOCUSID)
>  IDA   IDA   IDA   IDA   IEA   NAS   NAS   NAS    NR   TAS   TAS   TAS
TAS
> 17268 18771 20473 81646 25714  1050 31883  9569  7020 17877 17878
17927
17928
>   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS  
TAS
>  2034  2494  3091  3394  4617   463  4654  4784  5813  5989  5991 
7023
>
>
> >
> >I read the vignettes, but am not sure on how to do the above.
> >
> >Thanks!
> >
> >Simon
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>

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