[BioC] reading data from Beadarray into R

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Sep 29 21:22:20 CEST 2010


On Wed, Sep 29, 2010 at 3:16 PM, Hajar Hassani Lahsinoui
<hajar.hassani at gmail.com> wrote:
> Hello everyone,
> I'm new to R. I've received data from a bead array, consisting of 24 samples.
> I've installed the beadarray package from bioconductor.
> The problem is that whenever I try to read the data into R it gives me an error message.
> I don't know what I'm doing wrong (checked the directory)

*which* directory, is the question.

> targets = read.table("BeadTypeFile.txt")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>  cannot open file 'BeadTypeFile.txt': No such file or directory

R is telling you that it can't find "BeadTypeFile.txt".

You are giving R a relative path to a file, so it tries to find the
file in the current directory R is running in.

To see which directory that is, type:

R> getwd()
## you'll see an answer here.

Is your BeadTypeFile.txt in the directory that is returned from `getwd()`?

If not, you can simply try to use the absolute path to the file for
your `read.table` call.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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