Hi Rob, Unfortunately some features of arrayQuality are not compatible with versions of Hexbin greater than 1.0.10 at the moment. The best way to solve this problem would be to install hexbin 1.0.10 either from Bioconductor 1.5 or from our web site at http://www.arrays.ucsf.edu/software/. Best, Agnes -----Original Message----- From: Rob J Goedman [mailto:goedman@mac.com] Sent: Sat 5/28/2005 8:13 AM To: bioconductor@stat.math.ethz.ch Cc: Paquet, Agnes Subject: maQualityPlots (qpHexbin) question Hi, Am I using the right versions of arrayQuality and hexbin in BioC 1.6? Package: arrayQuality Version: 1.0.11 Date: 2005-04-10 Package: hexbin Version: 1.2.7 Date: 2005-04-06 Working through the 'Quick start guide for marray' I ran into a problem in step 6 [ library(arrayQuality); maQualityPlots(mraw) ]: Error in seq.default(0, 1, length = min(17, maxcnt)) : length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf Traceback shows it is in qpHexbin and looking at the function and documentation shows bin is an S4 object of class hexbin and mac$cnt this cannot access the slot 'count'. After fixing that, it runs into: Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hexagons" Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hex.legend" Which I also changed as in below file qpHexbin.R. The library version I've renamed qpHexbin-orig.R. Rob ??