Hi Djie: 

I´ve tried but I got another error..... 

Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument 

Any more ideas? 

Thanks a lot 

Juan 

--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de Biología Celular y Molecular 
Facultad de Ciencias-Universidade da Coruña 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@udc.es 
---------------------------------------------------------------- 



De: "Djie Tjwan Thung" <djie.thung@gmail.com> 
Para: "Juan Fernández Tajes" <jfernandezt@udc.es> 
CC: Bioconductor@r-project.org 
Enviados: Miércoles, 9 de Mayo 2012 13:27:55 
Asunto: Re: [BioC] Human Illumina Methylation27k question 

Hi Juan, 

Try the lumiMethyR function for reading in your final report instead of using the lumiR function. 

I.e.: 
library(lumi) 
fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' 
x.lumi <- lumiMethyR(fileName) 

Good luck! 

Djie 



2012/5/9 Juan Fernández Tajes < jfernandezt@udc.es > 


Dear list, 

It is possible to import GenomeStudio v1 data into R with lumi package? The headers in my GenomeStudio final report are these: 

AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. 

The code that I followed: 

library(lumi) 
fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' 
x.lumi <- lumiR.batch(fileName, columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) 

The error that I got: 

Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : 
Different column numbers of exprs and se.exprs! Please check the input data format. 

my sessionInfo(): 

R version 2.14.0 (2011-10-31) 
Platform: i386-apple-darwin9.8.0/i386 (32-bit) 

locale: 
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 

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

other attached packages: 
[1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 

loaded via a namespace (and not attached): 
[1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 BiocInstaller_1.2.1 DBI_0.2-5 
[7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 lattice_0.20-6 MASS_7.3-18 
[13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 RSQLite_0.11.1 tools_2.14.0 
[19] xtable_1.7-0 zlibbioc_1.0.1 

Any help would be very appreciated 

Juan 

--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de Biología Celular y Molecular 
Facultad de Ciencias-Universidade da Coruña 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@udc.es 
---------------------------------------------------------------- 



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