[BioC] LumiMouseV1 error

[Shawn Westaway]

Hi Paul,
Sorry it took me so long to duplicate your session info below. Here it
is - looks as if I have a more recent version of things?

Thanks
Shawn

> sessionInfo()
R version 2.5.0 (2007-04-23) 
powerpc-apple-darwin8.9.1 

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
lumiMouseV1       limma        lumi    annotate        mgcv        affy

    "1.2.0"    "2.10.0"     "1.2.0"    "1.14.1"    "1.3-23"    "1.14.0"

     affyio     Biobase 
    "1.4.0"    "1.14.0" 
> 



>>> "Paul Leo" <p.leo at uq.edu.au> - 5/3/07 4:39 PM >>>
I have used the lumi package recently and did not get this error (see
below). However I did note that the lumi annotation was somewhat
incomplete. May of the nuid's just returned "NA" when I asked for the
actual annotations (description or LL or SYMBOL). So I also used the
Illumina provided annotation file to fill in these gaps. 

Strangely the web site introducing the NUID's did have actual
annotations for some of these problem niud's. So I don't think the
lumiMouseV1 on the Bioconductor web site has the latest work???

How does your version differ to what I have used..(see below)

Cheers
Paul


>  lumi.N <- addNuId2lumi(lumi.N, lib = "lumiMouseV1")  
Loading required package: lumiMouseV1
> sessionInfo()
R version 2.5.0 alpha (2007-03-27 r40912) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

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

other attached packages:
lumiMouseV1        lumi        mgcv        affy      affyio     Biobase

    "1.1.1"     "1.0.7"    "1.3-23"   "1.13.18"     "1.3.3"   "1.13.46"


ALSO:array versions

# > x.lumi
# Data Information:
#         Illumina Inc. BeadStudio version 2.3.41
#         Normalization = none
#         Array Content = Mouse-6_v1_1_11234304_A.xml.xml
#         Error Model = none
#         DateTime = 20/02/2007 2:57 PM
#         Local Settings = en-AU
#         
# Major Operation History:
#             submitted            finished
# 1 2007-03-01 22:33:20 2007-03-01 22:33:34
#
command
# 1 lumiR("C:ResearchMicroArrayFraser group IlluminaDelivery 20-2-07
TinaLEC-JW-BeadStudioV2DataGS-GX
Format-NoneLEC-JW-BeadStudioV2_Sample_Gene_Profile.txt")
# 
# Object Information:
# LumiBatch (storageMode: lockedEnvironment)
# assayData: 46628 features, 6 samples 
#   element names: beadNum, detection, exprs, se.exprs
# phenoData
#   rowNames: A, B, ..., F (6 total)
#   varLabels and varMetadata:
#     sampleID: The unique Illumina microarray Id
#     label: The label of the sample
# featureData
#   rowNames: 10181072_239_rc-S, 10181072_290_rc-S, ..., YFP_luxY-S
(46628 total)
#   varLabels and varMetadata:
#     TargetID: The Illumina microarray identifier
#     presentCount: The number of detectable measurements of the gene
# experimentData: use 'experimentData(object)'
# Annotation character(0)
# > x.lumi$sampleID
# [1] "1735640002" "1735640002" "1735640002" "1735640002" "1735640002"
# [6] "1735640002"
>
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Shawn
Westaway
Sent: Thursday, 3 May 2007 9:02 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] LumiMouseV1 error

Dear Bioc. List,
I am getting an error message when uploading my mouse microarray data:

Warning messages:
1: Identifiers:3410269,3480281,3580285,3640290,3680294,3690297,3720306
cannot be found in the lumiMouseV1! in: addNuId2lumi(x.lumi, lib =
lib)

2: Duplicated IDs found and were merged! in: addNuId2lumi(x.lumi, lib
=
lib) 

I am wondering if anyone knows about error 1 or has a fix. I am not
sure if error 2 is of any concern.
Thanks,
Shawn

Shawn K. Westaway, Ph.D.
Research Assistant Professor
Department of Molecular and Medical Genetics
Oregon Health & Science University
Mailcode L103A
3181 SW Sam Jackson Park Road
Portland, Oregon USA 97239-3098
Office: 503-494-4344
Lab: 503-494-5326

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