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

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_M ON ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.12 52 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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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_M ON ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.12 52 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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor