Hello BioC community:

I am having trouble with lumiMouseV1. I am able to go from ID ->
ENTREZID via lumiMouseV1ENTREZID:

> entrezIds <- mget(featureNames(lumi.N), envir =
lumiMouseV1ENTREZID,ifnotfound=NA)
> head(entrezIds)
$iSh39ilew_g4tR.A18
[1] 78928

$`GI_10304988-S`
[1] NA

$oS6QgIgopJKKQ4S9Ko
[1] 16728

$`GI_12963686-S`
[1] NA

$`GI_12963764-I`
[1] NA

$`GI_13385605-S`
[1] NA

However, when I do the same for ID -> GO, every entry is NA.

> haveGO <-mget(featureNames(lumi.N), lumiMouseV1GO,ifnotfound=NA)
> head(haveGO)
$iSh39ilew_g4tR.A18
[1] NA

$`GI_10304988-S`
[1] NA

$oS6QgIgopJKKQ4S9Ko
[1] NA

$`GI_12963686-S`
[1] NA

$`GI_12963764-I`
[1] NA

$`GI_13385605-S`
[1] NA

(This is just a snippet, but they are all NA)

Looking at the info for LumiMouseV1() shows

> lumiMouseV1()

Quality control information for  lumiMouseV1 
Date built: Created: Fri Sep 14 10:29:15 2007  
 
Number of probes: 39562 
Probe number missmatch: None 
Probe missmatch: None 
Mappings found for probe based rda files: 
         lumiMouseV1ACCNUM found 39562 of 39562
         lumiMouseV1CHRLOC found 27910 of 39562
         lumiMouseV1CHR found 30304 of 39562
         lumiMouseV1ENTREZID found 30322 of 39562
         lumiMouseV1ENZYME found 3017 of 39562
         lumiMouseV1GENENAME found 30322 of 39562
         lumiMouseV1GO found 25323 of 39562
         lumiMouseV1MAP found 28678 of 39562
         lumiMouseV1PATH found 6548 of 39562
         lumiMouseV1PMID found 29523 of 39562
         lumiMouseV1REFSEQ found 29944 of 39562
         lumiMouseV1SUMFUNC found 0 of 39562
         lumiMouseV1SYMBOL found 30322 of 39562
         lumiMouseV1UNIGENE found 29391 of 39562 
Mappings found for non-probe based rda files:
         lumiMouseV1CHRLENGTHS found 21
         lumiMouseV1ENZYME2PROBE found 758
         lumiMouseV1GO2ALLPROBES found 7796
         lumiMouseV1GO2PROBE found 5614
         lumiMouseV1ORGANISM found 1
         lumiMouseV1PATH2PROBE found 192
         lumiMouseV1PFAM found 23763
         lumiMouseV1PMID2PROBE found 104537
         lumiMouseV1PROSITE found 16873 
Mappings from Illumina Identifiers to nuIDs:
        lumiMouseV1PROBEID2NUID: from Illumina Probe Id to nuID
        lumiMouseV1TARGETID2NUID: from Illumina Target Id to nuID


It appear that the there is nothing in lumiMouseV1GO. If you convert it
to a list, it just shows list(). 
This doesn't happen with lumiMouseV1ENTREZID. Looking at the lengths
shows this.

> length(lumiMouseV1ENTREZID)
[1] 39562

> length(lumiMouseV1GO)
[1] 0
> 
I have tried the exact same thing with lumiHumanV2GO (and different data
set), and it works. So I think I have the right idea, but may be
overlooking something obvious. Any help would be greatly appreciated.

Thanks,
Wade


J. Wade Davis, Ph.D.
Assistant Professor of Biostatistics
University of Missouri



Below is my session info.


> sessionInfo()
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
methods   base     

other attached packages:
 [1] lumiHumanV2_1.3.1       illuminaMousev1p1_1.4.0
illuminaMousev1_1.4.0   affycoretools_1.10.2   
 [5] gcrma_2.10.0            matchprobes_1.10.0      biomaRt_1.12.2
RCurl_0.8-1            
 [9] GOstats_2.4.0           Category_2.4.0          genefilter_1.16.0
survival_2.34          
[13] RBGL_1.14.0             GO.db_2.0.2             graph_1.16.1
annaffy_1.10.1         
[17] GO_2.0.1                KEGG_2.0.1              XML_1.93-2.1
limma_2.12.0           
[21] lumiMouseV1_1.3.1       lumi_1.4.0              annotate_1.16.1
xtable_1.5-2           
[25] AnnotationDbi_1.0.6     RSQLite_0.6-7           DBI_0.2-4
mgcv_1.3-29            
[29] affy_1.16.0             preprocessCore_1.0.0    affyio_1.6.1
Biobase_1.16.3         
[33] RWinEdt_1.7-9          

loaded via a namespace (and not attached):
[1] cluster_1.11.9



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