Question

Lumi problem

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mali salmon ▴ 370

@mali-salmon-4532

Last seen 5.5 years ago

Israel

I forgot to add sessionInfo() > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] genefilter_1.32.0 gplots_2.8.0 caTools_1.11 [4] bitops_1.0-4.1 gdata_2.8.1 gtools_2.6.2 [7] statmod_1.4.8 lumiMouseAll.db_1.12.0 org.Mm.eg.db_2.4.6 [10] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 [13] DBI_0.2-5 annotate_1.28.0 AnnotationDbi_1.12.0 [16] limma_3.6.9 lumi_2.2.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 hdrcde_2.15 [4] KernSmooth_2.23-4 lattice_0.19-13 MASS_7.3-9 [7] Matrix_0.999375-46 methylumi_1.6.1 mgcv_1.7-2 [10] nlme_3.1-97 preprocessCore_1.12.0 splines_2.12.1 [13] survival_2.36-2 tcltk_2.12.1 tools_2.12.1 [16] xtable_1.5-6 On Tue, Mar 8, 2011 at 9:23 AM, mali salmon <shalmom1@gmail.com> wrote: > Hi All > I am analysing illumina array data using "Lumi", and I found a problem with > adding control data to Lumi. > I have tried: > > >addControlData2lumi("illuminaControls.txt",x.lumi) > and got the following message: > "Annotation columns are not available in the data". > > Then I tried to create the LumiBatch by specifing the mouse annotation > library > >x.lumi<-lumiR("illuminaAll.txt",lib="lumiMouseAll.db") > >addControlData2lumi("illuminaControls.txt",x.lumi) > > but it didn't help, when I try to do background correction, I still get the > error: > "There is no control probe information in the LumiBatch object! > No background adjustment will be performed." > > Any ideas? > Thanks > Mali > > > -- Mali Salmon-Divon PhD EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD tel +44 (0)1223 494444 fax +44 (0)1223 494468 [[alternative HTML version deleted]]

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ADD COMMENT • link 13.1 years ago mali salmon ▴ 370

score 0 · Answer 1 · 2011-03-08

Hi All I am analysing illumina array data using "Lumi", and I found a problem with adding control data to Lumi. I have tried: >addControlData2lumi("illuminaControls.txt",x.lumi) and got the following message: "Annotation columns are not available in the data". Then I tried to create the LumiBatch by specifing the mouse annotation library >x.lumi<-lumiR("illuminaAll.txt",lib="lumiMouseAll.db") >addControlData2lumi("illuminaControls.txt",x.lumi) but it didn't help, when I try to do background correction, I still get the error: "There is no control probe information in the LumiBatch object! No background adjustment will be performed." Any ideas? Thanks Mali [[alternative HTML version deleted]]

score 0 · Answer 2 · 2011-03-08

Mali, One start is to use a lumi*IDMapping package instead, as shown below. ## load the data matt_exp <- lumiR(fileName,lib.mapping="lumiHumanIDMapping") I've also had intermittent problems with the function addControlData2lumi, and have used the alternate route below to get the info into the controlData slot. I have NOT looked at the source code of the addControlData2lumi function for a few years, but this should, in theory, be doing the same thing...or at least getting the same end result. But in my experience, this gives me less trouble. ################################ #Add QC Info ################################ controlFile <- paste(filedir,'QC.txt',sep="") controlData<-getControlData(controlFile, type = "data.frame") matt_exp at controlData<-controlData Good luck, Wade Davis -----Original Message----- From: mali salmon [mailto:shalmom1@gmail.com] Sent: Tuesday, March 08, 2011 1:30 AM To: bioconductor at r-project.org Subject: Re: [BioC] Lumi problem I forgot to add sessionInfo() > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] genefilter_1.32.0 gplots_2.8.0 caTools_1.11 [4] bitops_1.0-4.1 gdata_2.8.1 gtools_2.6.2 [7] statmod_1.4.8 lumiMouseAll.db_1.12.0 org.Mm.eg.db_2.4.6 [10] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 [13] DBI_0.2-5 annotate_1.28.0 AnnotationDbi_1.12.0 [16] limma_3.6.9 lumi_2.2.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 hdrcde_2.15 [4] KernSmooth_2.23-4 lattice_0.19-13 MASS_7.3-9 [7] Matrix_0.999375-46 methylumi_1.6.1 mgcv_1.7-2 [10] nlme_3.1-97 preprocessCore_1.12.0 splines_2.12.1 [13] survival_2.36-2 tcltk_2.12.1 tools_2.12.1 [16] xtable_1.5-6 On Tue, Mar 8, 2011 at 9:23 AM, mali salmon <shalmom1 at="" gmail.com=""> wrote: > Hi All > I am analysing illumina array data using "Lumi", and I found a problem with > adding control data to Lumi. > I have tried: > > >addControlData2lumi("illuminaControls.txt",x.lumi) > and got the following message: > "Annotation columns are not available in the data". > > Then I tried to create the LumiBatch by specifing the mouse annotation > library > >x.lumi<-lumiR("illuminaAll.txt",lib="lumiMouseAll.db") > >addControlData2lumi("illuminaControls.txt",x.lumi) > > but it didn't help, when I try to do background correction, I still get the > error: > "There is no control probe information in the LumiBatch object! > No background adjustment will be performed." > > Any ideas? > Thanks > Mali > > > -- Mali Salmon-Divon PhD EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD tel +44 (0)1223 494444 fax +44 (0)1223 494468 [[alternative HTML version deleted]]