[BioC] help with ath1121501

[James W. MacDonald]

Martin Olivier wrote:
> Hi all,
> 
> I have (again) some problems to use the package ath1121501.
> I don't understand the difference between ath1121501G02PROBE and
> ath1121501GO2ALLPROBES...

The difference is outlined in the help page for these two environments:

      ath1121501GO2PROBE is an R environment that provides mappings
      between GO identifiers and manufacturer identifiers.

      ath1121501GO2ALLPROBES is an R environment that provides mappings
      between a given GO identifier and all manufactuerer identifiers
      annotated at that GO term or one of its children in the GO
      ontology.

So if you want to map from a GO term to a probe ID, you would likely 
want the GO2PROBE environment.

Best,

Jim


> 
> I made a list listGO2GENE to have for each term GO all the genes that belong
> to this term GO. For this, I use ath1121501G02PROBE  or
> ath1121501GO2ALLPROBES. The problem is that the result depends on the choice
> between ath1121501G02PROBE  or ath1121501GO2ALLPROBES.
> 
> For example, if I use ath1121501G02PROBE, listGO2GENE["GO:0008104"] gives me
> three genes in the the GO term GO:0008104
> $"GO:0008104"
> [1] "AT1G48090" "AT3G50380" "AT5G24740"
> 
> and if I use ath1121501GO2ALLPROBES, I obtain more than 570 genes
> for this GO term...
> 
> So what is the right file I have to use to obtain the list that gives me 
> all the genes
> (in TAIR format) for a particular GO term.
> 
> 
> Here under, I give you the code  I used  to obtain the list 
> listGO2GENE...may be
> the pb is in my code??But it corresponds to a part of the code GOHyperG, 
> so it
> would be right...
> 
> goV<-mget(ls(ath1121501GO2PROBE),ath1121501GO2PROBE)
> listGO2GENE<- sapply(goV, function(x) {
>   if (length(x) == 0 || is.na(x))
>     return(NA)
>   lls <- unique(unlist(mget(x, 
> get("ath1121501LOCUSID",mode="environment"))))
>   lls <- lls[!is.na(lls)]
>   lls
> })
> 
> 
> Thanks for your help,
> Olivier.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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