Dear Sean, Thanks for your quick reply. After more investigation, I found out what the problem was. It turns out that prior to the switch to 20-bit scans (so nothing to do with that) our scanner was upgraded and all of the settings were changed. At the time the files switched to a different format which does not include some of the columns the default read.maimages function uses for source="agilent" (specificially, the files now completely lack "gMeanSignal" and "rMeanSignal" values.) I prefer to use the gMedianSignal and rMedianSignal anyway and will continue to do so by specifying the column definition as you suggested. (I was previously using a different program for processing array data and I am switching over to limma so thanks for your help, it's much appreciated! Ilsa ________________________________ From: Sean Davis [mailto:seandavi@gmail.com] Sent: Wednesday, February 04, 2009 4:00 PM To: Coleman, Ilsa Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for 20-bit scanner? On Wed, Feb 4, 2009 at 6:39 PM, Coleman, Ilsa <icoleman@fhcrc.org> wrote: Hi, I can read in 2-color Agilent data from 16-bit scans (Agilent Technologies Scanner G2505B) using read.maimages(limma) source="agilent" but for some reason cannot read in data files from 20-bit scans (Agilent Technologies Scanner G2505C). This probably has to do with the fact that the 20-bit scans no longer require two scans (low and high) so there are fewer data columns in these files. Has anyone else had this problem and is there a plan to update the read.maimages(limma) function? Hi, Ilsa. You can specify the columns to read using read.maimages. See the help page for a great deal of detail. Sean [[alternative HTML version deleted]]