Hi Pan Du,
I just tried to import some of my Illumina data using you nice lumi
package. However, lumiR stopped with an error message. When debugging
the function I noticed that the problem is in the decimal separator that
is used for numeric data. For the output on a German PC BeadStudio uses
commas as decimal separators (which is for some strange historic reason
the German convention...). Now the following will produce a matrix of
NAs since R doesn't know how to convert e.g. 1,2312 to a numeric
if (!is.numeric(exprs[1])) {
exprs <- matrix(as.numeric(exprs), nrow = nrow(allData))
}
My rather naiv approach of fixing this is to include the following:
if (!is.numeric(exprs[1])) {
exprs <- gsub(",", ".", exprs, fixed=TRUE)
exprs <- matrix(as.numeric(exprs), nrow = nrow(allData))
}
Of course the same needs to be done for the other numeric columns as
well. There might be a more elegant way to figure out the separator and
fix this already before.
Hope this helps in your development process,
Florian
R version 2.6.0 Under development (unstable) (2007-06-11 r41910)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] tcltk tools stats graphics grDevices datasets utils
[8] methods base
other attached packages:
[1] debug_1.1.0 mvbutils_1.1.1 lumi_1.3.13
[4] annotate_1.15.2 AnnotationDbi_0.0.78 RSQLite_0.5-4
[7] DBI_0.2-3 mgcv_1.3-24 affy_1.15.7
[10] preprocessCore_0.99.7 affyio_1.5.4 Biobase_1.15.14
loaded via a namespace (and not attached):
[1] rcompgen_0.1-13