Hi Bioconducter: I ran expresso of Affy package on R version 2.1.0 as below: > dataRMA_norm_loess <- expresso(data, bgcorrect.method="rma", + normalize.method="loess", pmcorrect.method="pmonly", summary.method="medianpolish") The error message I got was: background correction: rma normalization: loess PM/MM correction : pmonly expression values: medianpolish background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) : no direct or inherited method for function 'bg.correct' for this call If I ran with bg.correct="rma" and left the rest the same, I got: Error in expresso(data, bg.correct = "rma", normalize.method = "loess", : unimplemented type 'character' in 'asLogical' Note: data is the loaded .CEL files from the estrogen package as well as the phenotypic data. Anything wrong? Thanks! JP- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin@email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx