[BioC] questions about agilent 44k array

[xuejun qin]

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!!