For anyone who deals with agilent data, a heads up - with the upgrade to Feature Extraction 10.1.1 (comes with scanner upgrade), the default text file output will be in the "COMPACT" text format, which leaves out the columns used by limma in read.maimages. In order to get all the columns, you have to select "FULL" in the Project Properties tab of Feature Extraction. Madelaine Gogol Programmer Analyst II Stowers Institute