[BioC] Human Illumina Methylation27k question

[Pan Du]

Hi Juan

The lumiMethyR function basically calls "methylumiR" function in
methylumi package. I believe the column names in your file do not
match the predefined format in the function. If possible, you can send
me the top 200 rows of your file or just send me zipped data file if
it is not too big. I can help you have a check.

An alternative way to input methylation data is using "methylumIDAT"
function to directly input the iDAT file. In this way you can avoid
the header format issues. Check the help of "methylumIDAT" function
for more details.


Pan


> Date: Wed, 9 May 2012 13:33:17 +0200 (CEST)
> From: Juan Fern?ndez Tajes <jfernandezt at udc.es>
> To: Djie Tjwan Thung <djie.thung at gmail.com>
> Cc: Bioconductor at r-project.org
> Subject: Re: [BioC] Human Illumina Methylation27k question
> Message-ID:
>        <736487667.320495.1336563197758.JavaMail.root at ms1a.correo.udc.es>
> Content-Type: text/plain
>
> 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 at udc.es
> ----------------------------------------------------------------
>
>
>
> De: "Djie Tjwan Thung" <djie.thung at gmail.com>
> Para: "Juan Fernández Tajes" <jfernandezt at udc.es>
> CC: Bioconductor at 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 at 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