[BioC] reading with lumi

[Ed Siefker]

I am trying to read Level 1 methylation data
from the TCGA into bioconductor.  The
platform is HumanMethylation27, which
is supported by lumi, right?

Here is my R session:

> library(lumi)
Loading required package: methylumi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: nleqslv
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: ‘lumi’

The following object(s) are masked from ‘package:methylumi’:

    estimateM, getHistory

Warning message:
found methods to import for function ‘as.list’ but not the generic itself
>
> fileName <- 'jhu-usc.edu_COAD.HumanMethylation27.1.lvl-1.TCGA-AA-3555-01A-01D-0820-05.txt'
> example.lumi <- lumiR(fileName)
Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
>