[BioC] problem reading raw data file with lumi

[Pan Du]

Hi Sebastien,

The reason lumiR reported error is that the 'raw_data.csv' provided in
BeadArray package was not originally outputted by BeadStudio (or because it
used a very old version). Some people might have manually modified the meta
information (or just typo) of the file. Also the data include the columns
with duplicated names.

For example:
In the raw_data.csv file, the first two lines are:
   I Inc. BeadStudio version 1.5.1.3
   Normization = none

There are two places seems manually changed by some people:
1. "I Inc." should be "Illumina Inc.";
2. "Normization" should be "Normalization".


Our previous lumiR version tried to verify whether the data was outputted
from BeadStudio. It reported error because of the above modification. In
order to make it more robust, we updated our code. Now the lumiR has no
problem to read the "raw_data.csv" file, but it will give some warning
message because of the problems of the data.

You can download the latest version from Bioconductor developing version,
which is version 1.3.13.
http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html

Thanks for reporting the problem!


Pan


------------------------------

Message: 16
Date: Fri, 22 Jun 2007 15:00:57 +1000
From: "Sebastien Gerega" <seb at gerega.net>
Subject: [BioC] problem reading raw data file with lumi
To: bioconductor at stat.math.ethz.ch
Message-ID:
    <5c5d36cf0706212200i7f2387f3v22fec45365cc12ed at mail.gmail.com>
Content-Type: text/plain

Hi,
when attempting to read a raw data file (BeadStudio) with lumi I obtained
the following error:

Error in lumiR("raw_data.csv") : attempt to select less than one element

The raw data file I am attempting to read is that provided as sample data
with the beadarray package (
http://bioconductor.org/packages/2.0/bioc/html/beadarray.html).

Does anyone know what is causing this error? Or has anyone experienced
anything similar? The file works perfectly when being read by beadarray.

thanks,
Sebastien Gerega

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