[BioC] problem with hyperGTest and ath1121501?

[Nianhua Li]

Hi, Seth and Martin,

I only know the ath1121501 part. "AT1G55530" etc are locus name
(standard AGI convention name), not gene symbols. proble set ID to AGI
locus mapping is provided in ath1121501ACCNUM, ath1121501ENTREZID, and
ath1121501LOCUSID. The last two are references to ath1121501ACCNUM. They
are there for compatiability with other software packages.  

> x <- as.list(ath1121501ACCNUM)
> genesel<-c("AT1G55530", "AT5G19770" ,"AT4G10840")
> index <- match(genesel, x)
> names(x)[index]
[1] "265077_at" NA          "254951_at"
> probesel <- names(x)[index]
> mget(probesel[!is.na(probesel)], ath1121501GO)
$`265077_at`
$`265077_at`$`GO:0005515`
$`265077_at`$`GO:0005515`$GOID
[1] "GO:0005515"

$`265077_at`$`GO:0005515`$Evidence
[1] "IEA"

$`265077_at`$`GO:0005515`$Ontology
[1] "MF"


$`265077_at`$`GO:0005515`
$`265077_at`$`GO:0005515`$GOID
[1] "GO:0005515"

$`265077_at`$`GO:0005515`$Evidence
[1] "ISS"

$`265077_at`$`GO:0005515`$Ontology
[1] "MF"


$`265077_at`$`GO:0008270`
$`265077_at`$`GO:0008270`$GOID
[1] "GO:0008270"

$`265077_at`$`GO:0008270`$Evidence
[1] "IEA"

$`265077_at`$`GO:0008270`$Ontology
[1] "MF"


$`265077_at`$`GO:0008270`
$`265077_at`$`GO:0008270`$GOID
[1] "GO:0008270"

$`265077_at`$`GO:0008270`$Evidence
[1] "ISS"

$`265077_at`$`GO:0008270`$Ontology
[1] "MF"



$`254951_at`
$`254951_at`$`GO:0009507`
$`254951_at`$`GO:0009507`$GOID
[1] "GO:0009507"

$`254951_at`$`GO:0009507`$Evidence
[1] "IEA"

$`254951_at`$`GO:0009507`$Ontology
[1] "CC"

I checked TAIR
(ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/) and Gene
Ontology and got the same GO IDs. The AGI locus given in this particular
example are not associated with any GO terms in Biological Process
category. Maybe you could try category MF or CC or try other AGI locus?

hope it helps

nianhua