Hi all, I'm having some difficulties using the read.marrayInfo method of the marrayInput package. Basically, I get an unusual error message after a few seconds of processing. ======================================================= > rat.layout <- read.marrayLayout(fname = fname, ngr=4, ngc=12, nsr=25, nsc=26, skip=53, ctl.col=4, pl.col=5); > rat.layout; Array layout: Object of class marrayLayout. Total number of spots: 31200 Dimensions of grid matrix: 4 rows by 12 cols Dimensions of spot matrices: 25 rows by 26 cols Currently working with a subset of 31200 spots. Control spots: There are 9935 types of controls : 3x SSC Arab Mm.10 Mm.100049 Mm.100060 Mm.10009 Mm.100099 Mm.100113 Mm.100117 Mm.100131 98 480 2 2 2 2 2 2 2 2 ... Notes on layout: c:/docume~1/paul/dev/input/GP_M15k1.gal > rat.names <- read.marrayInfo(fname=fname, info.id=5, labels=5, skip=53); Error in "maInfo<-"(*tmp*, value = dat[, info.id]) : No direct or inherited method for function "maInfo<-" for this call > traceback(); 2: "maInfo<-"(*tmp*, value = dat[, info.id]) 1: read.marrayInfo(fname = fname, info.id = 5, labels = 5, skip = 53) ======================================================= I'm not too clear what's going on here. In case it helps, here is the first bit of my GAL input file. ATF 1.0 51 5 Type=GenePix ArrayList V1.0 BlockCount=48 BlockType=0 "Block1= 3000, 3000, 110, 26, 167, 25, 167" "Block2= 7500, 3000, 110, 26, 167, 25, 167" "Block3= 12000, 3000, 110, 26, 167, 25, 167" "Block4= 16500, 3000, 110, 26, 167, 25, 167" "Block5= 3000, 7500, 110, 26, 167, 25, 167" "Block6= 7500, 7500, 110, 26, 167, 25, 167" "Block7= 12000, 7500, 110, 26, 167, 25, 167" "Block8= 16500, 7500, 110, 26, 167, 25, 167" "Block9= 3000, 12000, 110, 26, 167, 25, 167" "Block10= 7500, 12000, 110, 26, 167, 25, 167" "Block11= 12000, 12000, 110, 26, 167, 25, 167" "Block12= 16500, 12000, 110, 26, 167, 25, 167" "Block13= 3000, 16500, 110, 26, 167, 25, 167" "Block14= 7500, 16500, 110, 26, 167, 25, 167" "Block15= 12000, 16500, 110, 26, 167, 25, 167" "Block16= 16500, 16500, 110, 26, 167, 25, 167" "Block17= 3000, 21000, 110, 26, 167, 25, 167" "Block18= 7500, 21000, 110, 26, 167, 25, 167" "Block19= 12000, 21000, 110, 26, 167, 25, 167" "Block20= 16500, 21000, 110, 26, 167, 25, 167" "Block21= 3000, 25500, 110, 26, 167, 25, 167" "Block22= 7500, 25500, 110, 26, 167, 25, 167" "Block23= 12000, 25500, 110, 26, 167, 25, 167" "Block24= 16500, 25500, 110, 26, 167, 25, 167" "Block25= 3000, 30000, 110, 26, 167, 25, 167" "Block26= 7500, 30000, 110, 26, 167, 25, 167" "Block27= 12000, 30000, 110, 26, 167, 25, 167" "Block28= 16500, 30000, 110, 26, 167, 25, 167" "Block29= 3000, 34500, 110, 26, 167, 25, 167" "Block30= 7500, 34500, 110, 26, 167, 25, 167" "Block31= 12000, 34500, 110, 26, 167, 25, 167" "Block32= 16500, 34500, 110, 26, 167, 25, 167" "Block33= 3000, 39000, 110, 26, 167, 25, 167" "Block34= 7500, 39000, 110, 26, 167, 25, 167" "Block35= 12000, 39000, 110, 26, 167, 25, 167" "Block36= 16500, 39000, 110, 26, 167, 25, 167" "Block37= 3000, 43500, 110, 26, 167, 25, 167" "Block38= 7500, 43500, 110, 26, 167, 25, 167" "Block39= 12000, 43500, 110, 26, 167, 25, 167" "Block40= 16500, 43500, 110, 26, 167, 25, 167" "Block41= 3000, 48000, 110, 26, 167, 25, 167" "Block42= 7500, 48000, 110, 26, 167, 25, 167" "Block43= 12000, 48000, 110, 26, 167, 25, 167" "Block44= 16500, 48000, 110, 26, 167, 25, 167" "Block45= 3000, 52500, 110, 26, 167, 25, 167" "Block46= 7500, 52500, 110, 26, 167, 25, 167" "Block47= 12000, 52500, 110, 26, 167, 25, 167" "Block48= 16500, 52500, 110, 26, 167, 25, 167" Block Row Column Name ID 1 1 1 Mm.142830 H3005F02 1 1 2 Mm.142830 H3005F02

Hi Paul, This is a bug in "read.marrayInfo" which I will fix for the next release. The problem arrive when you select only one column for info.id. For the moment, one fix is to select both column 4 and 5 of your gal file into the marray Info rat.names <- read.marrayInfo(fname=fname, info.id=4:5, labels=5, skip=53); Alternatively, you can edit the read.marrayLayout at the line maInfo(descript) <- dat[,info.id] to be maInfo(descript) <- as.data.frame(dat[,info.id]) Cheers Jean