[BioC] lumiMouseV1 trouble

[Pan Du]

Hi Davis,

Based on your script returns, I guess your mouse chip version is not version
1 because lots of TargetIDs cannot be found in the lumiMouseV1 library. So
please check your chip version first. If you are using Illumina Mouse
Version 2, then you cannot use lumiHumanV1. You should use lumiHumanAll.db
or illuminaMousev2ProbeID.db.

Another suggestion is to use "Sample Probe Profile.txt" (ProbeID indexed)
instead of "Sample Gene Profile.txt" (TargetID indexed).

Please read the lumi vignette for more details.


Pan


On 5/17/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 3
> Date: Fri, 16 May 2008 09:49:56 -0500
> From: "Davis, Wade" <davisjwa at health.missouri.edu>
> Subject: [BioC] lumiMouseV1 trouble
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <09E4AABB118D2C47AEDFC6210BF1DEA902F2A2EB at UM-XMAIL02.um.umsystem.edu>
> Content-Type: text/plain
> 
> 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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