I would like to know how to run PRvQCHyb in arrayQuality. I copied four gpr files into a same directory. They were from the same print run. PRv9mers() worked fine, but PRvQCHyb () had 'invalid regular expression' error. If I specified one file name, then it generated only one picture file with the file size 0 and subscript out of bounds error. Could you help to use PRvQCHyb? Thank you. Wonjong ---------------------------- I pasted what I did from the R screen ------------------------------------ > library(arrayQuality) Loading required package: marray Loading required package: limma Loading required package: convert Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: hexbin Loading required package: grid Loading required package: lattice Loading required package: colorspace Loading required package: gridBase Loading required package: RColorBrewer > PRv9mers() [1] "./xMmPRQC" [1] "in the loop" [1] "jchen_13583932_2007-02-26.split_one.channel_switch.gpr" Reading ... ./jchen_13583932_2007-02-26.split_one.channel_switch.gpr Loading required package: mclust [1] TRUE save as P9mers.jchen_13583932_2007-02-26.split_one.channel_switch.png [1] "in the loop" [1] "jchen_13583932_2007-02-26.split_two.channel_switch.gpr" Reading ... ./jchen_13583932_2007-02-26.split_two.channel_switch.gpr [1] TRUE save as P9mers.jchen_13583932_2007-02-26.split_two.channel_switch.png [1] "in the loop" [1] "jchen_13583934_2007-02-26.split_one.channel_switch.gpr" Reading ... ./jchen_13583934_2007-02-26.split_one.channel_switch.gpr [1] TRUE save as P9mers.jchen_13583934_2007-02-26.split_one.channel_switch.png [1] "in the loop" [1] "jchen_13583934_2007-02-26.split_two.channel_switch.gpr" Reading ... ./jchen_13583934_2007-02-26.split_two.channel_switch.gpr [1] TRUE save as P9mers.jchen_13583934_2007-02-26.split_two.channel_switch.png Extracting missing probes Done > PRvQCHyb() [1] "Starting PRvQCHyb" Error in list.files(path, pattern, all.files, full.names, recursive) : invalid 'pattern' regular expression > PRvQCHyb(fnames="jchen_13583934_2007-02-26.split_one.channel_switch.gp > r") [1] "Starting PRvQCHyb" Reading ... ./jchen_13583934_2007-02-26.split_one.channel_switch.gpr [1] TRUE [1] TRUE Error in eval(expr, envir, enclos) : subscript out of bounds