[BioC] question about read.marrayRaw

[Gustavo Henrique Esteves]

Hello Ren,

Try to set the maSub in your marrayLayout object to a vector of TRUEs
with length equal to the number of spots you have in your files. I
have had the same problem and doing this resolved to me.

Well hapened to me in R-1.9.1 with the last marray package. In the
previous versions I didn't have this problem. What version of R /
marray are you using?

Gustavo




On Fri, 01 Oct 2004 16:46:03 -0500, Ren Na <na at uthscsa.edu> wrote:
> 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
> ...............................................................................
> ...............................................................................
> I couldn't figure out what I did wrong. Thanks for any help.
> 
> Ren
> 
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> 



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Gustavo Henrique Esteves

e-mail: gesteves at gmail.com
Home Page: http://www.vision.ime.usp.br/~gesteves/