Hello, 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

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. Cheers Alice Ps also when you are posting for help with BioC put in your email the output of >sessionInfo() And the error messages that you have so you get prompt help! -----Original Message----- From: bioconductor-bounces@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 Hello, 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 P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.