[BioC] question about read.marrayRaw

[Ren Na]

Gustavo Henrique Esteves wrote:

>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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>>
>>    
>>
>
>
>
>  
>
Hi, Gustavo,
Thank you very much, it works with your suggestion.
I had exactly same experience like you. I am using R(1.9.1) and the last 
marray package(1.5.14). And I didn't have this problem before.

Ren