[BioC] question about read.marrayRaw

Ren Na na at uthscsa.edu
Fri Oct 1 23:46:03 CEST 2004


I try to create a marrayRaw object. The problem I am having is that only 
the first line of  my every .spot file has been read by the function 
read.marrayRaw. The following is what I did,
xpd.layout <- read.marrayLayout(fname="Mouse24052004.txt", ngr=8, ngc=4, 
nsr=23, nsc=23, skip=0, ctl.col=6)
xpd.samples<- read.marrayInfo("sample.txt")
xpd.gnames<-read.marrayInfo("Mouse24052004.txt", info.id=6, labels=10, 
skip=0)
targets <- readTargets("Targets.txt")
fnames<-targets$FileName
xpd.raw<-read.marrayRaw(fnames, name.Gf="Gmedian", name.Gb="morphG", 
name.Rf="Rmedian", name.Rb="morphR", layout=xpd.layout, 
gnames=xpd.gnames, targets=xpd.samples)
 > xpd.raw
An object of class "marrayRaw"
@maRf
     ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot
[1,]         621         217         639         539         329         290
     ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot
[1,]        1704         198         606         563         562        1052
     ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot
[1,]         817         101         297         433        1926         650

@maGf
     ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot
[1,]         380         657         555         554         638         346
     ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot
[1,]        3267         349         503         635         844        1596
     ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot
[1,]        1078          90         334         549        2118        1093

@maRb
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I couldn't figure out what I did wrong. Thanks for any help.

Ren



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