Hi, dear all, I need you guys help, I got array data in Agilent 44k format, it has number for columns and rows but no number for grid, there is a lot of missing data, that means different numbers of spot for each row, but all array have same number of spots. I try to clean the data by package of marray. as following NTD.layout <- read.marrayLayout(fname = file.path(datadir,"agi.txt"), ngr = 1, ngc = 1, nsr =43931, nsc = 1, skip = 1) ## ngr=1, ngc=1, which can import all data, as there is different number of spots for each row, I set nsc=1 NTD.gnames <- read.marrayInfo(fname=file.path(datadir,"agi.txt"), info.id=4:5,labels=4) NTD.samples <- read.marrayInfo(fname=file.path(datadir,"tempgets1.txt"), info.id=1:5,labels=3) nameTab <- read.table("tempnames.txt",header=TRUE,sep="\t",quote="\"" fnames <- as.character(nameTab$FileName) NTD.raw <- read.marrayRaw(fnames,path=datadir,skip=NULL, name.Gf="gMeanSignal",name.Gb="gBGMedianSignal",name.Rf="rMeanSignal", name.R b="rBGMedianSignal",layout=NTD.layout, gnames=NTD.gnames,targets=NTD.samples) Rcol <- maPalette(low="white",high="red") Gcol <- maPalette(low="white",high="green") image(NTD.raw[,1],yvar="maRb",col=Rcol,main=maLabels(maTargets(NTD.raw [1,j]) ),contours=TRUE,bar=TRUE) Error in image.default(1:nc, 1:nr, z, axes = FALSE, col = col, ...) : `z' must be a matrix I know if I set number for ngr, ngc other than 1, it works, but that means I lost some data. I try to get the graph to check quality of data, such as Rb, Gb, Rf, Gf, also I want to check those Rb>Rf , Gb>Gf, but marrayTwo doesn't exist anymore . Any suggestion about Agilent 44k data will be welcome. Thank You!!