[BioC] Lumi problem

[Davis, Wade]

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 at 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

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