Today I wrote to Rafael Irizarry about this and he suggested I post my message here. Some time back I wrote some R code to normalise from one to several tens of thousand Affymetrix cel files on a (Linux) PC. The advantage is that it does not keep all cel files in memory all the time and so the usual memory limits which restrict the number of cel files do not apply. http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp- code/R/TCBB-2007-11-0161_noCEL.tar The R-code also reports spatial defects: A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips, W. B. Langdon and G. J. G. Upton and R. da Silva Camargo and A. P. Harrison, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(4) 647-653 oct-dec 2010. PubMed 21030732 If we could incorporate this into your bioconductor affy package that would be great. Bill Dr. W. B. Langdon, Department of Computer Science, University College London Gower Street, London WC1E 6BT, UK http://www.cs.ucl.ac.uk/staff/W.Langdon/ -- output of sessionInfo(): n/a -- Sent via the guest posting facility at bioconductor.org.