[BioC] readBeadSummaryData() in beadarray package

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Wed Jan 23 19:49:39 CET 2008

Hi Daniel
I think what you are having problems with is the same thing that I did,
instead of using Illuminas Target ID column, you need to use the ProbeID
column as some of the TargetIDs can be repeated.

Ps also when you are posting for help with BioC put in your email the
output of 
And the error messages that you have so you get prompt help!

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Daniel Pick
Sent: Wednesday, 23 January 2008 8:21 p.m.
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] readBeadSummaryData() in beadarray package

   I have beadarray version 1.6 installed on R 2.6.1.  I am trying to
read bead  summary data using the readBeadSummaryData() command.  I have
successfully read the dats in the example file that comes with the
beadarray package, but now I am trying to read in a different data file.
   The data set has no lines to skip at the top of the file, so I have
set the skip parameter to 0.  Also, the file only has four columns which
correspond to the exprs, se.exprs, Detection, and NoBeads slots, but
with different column headings than the defaults, so I have changed the
column names appropriately.
The first column in the file is labeled "TargetID", which corresponds to
the default setting for the ProbeID parameter.
   However, when R tries to read the data, it's choking on the rownames
assignment statement in the code.  I have attached a small sample of the
data file in Excel spreadsheet format, so people can see it.  Can anyone
explain  the correct format of the readBeadSummaryData() command to read
this data?

--Daniel Pick

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