[Bioc-devel] read.maimages, limma

Martin Maechler maechler at stat.math.ethz.ch
Tue Apr 12 14:58:53 CEST 2005

>>>>> "Tarca" == Tarca Adi Laurentiu <ltarca at biota.rsvs.ulaval.ca>
>>>>>     on Mon, 11 Apr 2005 16:08:39 -0400 writes:

    Tarca> Hi everyone,

    Tarca> I am using R.2.1.0 with limma 1.8.18 to read a "quantarray" .txt file.
    >> RG <- read.maimages(file,source="quantarray")
    Tarca> Error in "[.data.frame"(obj, , columns$Rf) :
    Tarca> undefined columns selected

    Tarca> The same data with the previous version of R (2.0.1) was working fine.
    Tarca> Does anyone have a suggestion?

Since you are from a place where é , à etc are not entirely
unreasonable: Could it be that you have non-ASCII characters in your data

If so, this could be the explanation: If your locale setting {
help(Sys.locale) } is unicode-ish {e.g. fr_CA.utf-8}, then
text connections will assume unicode rather than iso-latin-*
encoding, unless you specify the encoding:

We had a similar problem with read.table where we needed to use
   read.table(file("foo.txt", encoding="LATIN1"), ........)
instead of
   read.table("foo.txt", ........)

Alternatively, you could set    options(encoding = "LATIN1")
before reading the files
{if almost all of your input file use ISO-latin-1 aka iso-8859-1 encoding}

Does that help?
Martin Maechler, ETH Zurich

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