[BioC] Run GOHyperG on yeast without specifying a chip

[maria at cbm.bio.uniroma2.it]

thanks James, I though that the identifiers with wich you succeeded were 
the systematic names....for me common names were the other ones NOT 
belonging with Y.

Best,

Maria

Maria Persico, PhD. student
http://cbm.bio.uniroma2.it/~maria/
MINT database group
Universita' di Tor Vergata, via della Ricerca scientifica 11
00133 Roma, Italy
Tel +39 0672594315 (Supervisor's room)
Fax +39 0672594766
Mobile phone: +393479715662
e-mail maria at cbm.bio.uniroma2.it

On Tue, 4 Jul 2006, James W. MacDonald wrote:

> Hi Maria,
>
> maria at cbm.bio.uniroma2.it wrote:
>>  Hello everyone,
>>
>>  I'm trying to calculate the probability that 2 YEAST proteins share the
>>  same biological process by chance as suggested in the Liu's paper (PMID
>>  15905281); I want a p-value associated to each protein pair in my data
>>  set; I would like to use the Bioconductor implementation of GO analysis:
>>  in the help page of the GOHyperG I read the following phrase:
>>
>>  " For S. cerevisiae if the 'lib' argument is set to '"YEAST"' then
>>  comparisons and statistics are computed using common names and are with
>>  respect to all genes annotated in the S. cerevisiae genome not with
>>  respect to any microarray chip."
>>
>>  this is exactly my case, I don't have a chip. I load the libraries GOstats
>>  and YEAST and I choose two common names of two proteins to see if the
>>  pipeline works:
>> 
>> > library(GOstats)
>> > library(YEAST)
>>
>> 
>> > myYCM<-c("RAD24","DMC1")
>>
>>
>>  At this point I got the following error message:
>>
>> 
>> > xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL)
>>
>>  Error in length(p at universeGeneIds) - numAtCat :
>>           non-numeric argument to binary operator
>>
>>  I suppose that the problem is the universe; what should I provide as
>>  universe value if comparisons and statistics are computed using common
>>  names....in the error message I see p at universeGeneIds!?
>
> I don't think that is the problem. I think the common names expected are 
> things like "YPL113C"   "YNL055C"   "YKL154W"   "YNR076W" (I believe these 
> are the Locus Tags?). If I look up the correct locus tags for your genes, 
> things work for me.
>
>>  myYCM<-c("YER173W", "YER179W")
>>  xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL)
>> 
>
> HTH,
>
> Jim
>
>
>>
>>  thanks,
>>
>>  Maria
>>
>>  Maria Persico, PhD. student
>>  http://cbm.bio.uniroma2.it/~maria/
>>  MINT database group
>>  Universita' di Tor Vergata, via della Ricerca scientifica 11
>>  00133 Roma, Italy
>>  Tel +39 0672594315 (Supervisor's room)
>>  Fax +39 0672594766
>>  Mobile phone: +393479715662
>>  e-mail maria at cbm.bio.uniroma2.it
>>
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>
>
> -- 
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
>
>
>
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