Thanks Wade, this trick indeed worked
Mali

On Tue, Mar 8, 2011 at 10:00 PM, Davis, Wade
<davisjwa@health.missouri.edu>wrote:

> 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@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@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@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
>
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>
>
>

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