[BioC] help with ath1121501

[John Zhang]

>
>I have (again) some problems to use the package ath1121501.
>I don't understand the difference between ath1121501G02PROBE and
>ath1121501GO2ALLPROBES...

GO2PROBE gives you the probes that are associated with a given GO id.

GO2ALLPROBES givens you the probes that associated with a given GO id + probes 
that associated with the GO ids that are the child-nodes of that GO id. 




>
>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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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084