Hi guys,

I was running lumi package to analyze the methylation data, and I used the
following scripts:

setwd('C:/Documents and Settings/xxx/My Documents/Downloads/HumanSamples')
library(lumi)
library(IlluminaHumanMethylation27k.db)
data0<- 'Sample Methylation Profile.txt'
sample.lumiMethy <- lumiMethyR(data0, lib="IlluminaHumanMethylation27k.db")

I can not read in the data. The error is shown below:

Error in if (mm < 0.01) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 1535Mb: see help(memory.size)
2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 1535Mb: see help(memory.size)
3: In slot(value, what) <- slot(from, what) :
  Reached total allocation of 1535Mb: see help(memory.size)
4: In slot(value, what) <- slot(from, what) :
  Reached total allocation of 1535Mb: see help(memory.size)

My sectionInfo is shown below:

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] IlluminaHumanMethylation27k.db_1.4.0
org.Hs.eg.db_2.4.6                   RSQLite_0.9-4
DBI_0.2-5
[5] AnnotationDbi_1.12.0
lumi_2.2.1                           Biobase_2.10.0
loaded via a namespace (and not attached):
 [1] affy_1.28.0           affyio_1.18.0         annotate_1.28.1
grid_2.12.2           hdrcde_2.15           KernSmooth_2.23-4
lattice_0.19-17
 [8] MASS_7.3-11           Matrix_0.999375-46    methylumi_1.6.1
mgcv_1.7-3            nlme_3.1-98           preprocessCore_1.12.0
tools_2.12.2
[15] xtable_1.5-6

I am using windowsXP SP3 32bit, and my memory size is 3.16Gb.

Any hint or suggestion will be much appreciated! Thanks a lot!

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