Hello, it's the first time I am dealing with two-color microarrays. That is why I have some (probably stupid) questions... I am trying to analyze GenePix files using the marrayInput package and I ran into two difficulties: 1) I have 24 GenePix-arrays that are defined by three different *.gal-files. Can I merge the expressions for these three types of arrays for the upcoming normalization step? 2) Does someone know the error message "Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed" and has a hint for avoiding it? > galinfo<-read.Galfile("3kArray5.gal") > myTargets <- read.marrayInfo(file.path(data.dir, "target.txt")) target.txt: Name Cy3 Cy5 a.gpr 10D 14D ar.gpr 14D 10D > read.GenePix(c("a.gpr","ar.gpr"),targets=myTargets,layout=galinfo$layo ut,gnames=galinfo$gnames,) Reading ... a.gpr Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed Unfortunately, I have no idea what could be the reason for this error message. I would be very glad about any suggestion. Thanks in advance and best wishes, Heike PS: I am using R2.3.1 and marray version 1.12.0. -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312

Hi Heike, > PS: I am using R2.3.1 and marray version 1.12.0. The first thing you need to do is to upgrade your R and install the latest marray package. Then give another try. If you still have problems, send another note. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org