16 May 16:49
lumiMouseV1 trouble
From: Davis, Wade <davisjwa@...>
Subject: lumiMouseV1 trouble
Newsgroups: gmane.science.biology.informatics.conductor
Date: 2008-05-16 14:49:56 GMT
Subject: lumiMouseV1 trouble
Newsgroups: gmane.science.biology.informatics.conductor
Date: 2008-05-16 14:49:56 GMT
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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