problem reading raw data file with lumi
1
0
Entering edit mode
@sebastien-gerega-2229
Last seen 8.1 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070622/ 154f9b15/attachment.pl
• 173 views
ADD COMMENT
0
Entering edit mode
Pan Du ★ 1.2k
@pan-du-2010
Last seen 8.1 years ago
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@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 [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 361 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6