Hi, I'm using marray packages in order to normalize my data. I load my data using the command lines : slide.layout=read.marrayLayout("~/tmp/ slides.Rlayout",ngr=8,ngc=4,nsr=20,nsc=20,ctl.col=6) slide.gnames=read.marrayInfo("~/tmp/slides.Rlayout",info.id=6, labels=5) slide.raw=read.marrayRaw("raw.csv",path="~/ tmp/",name.Gf="f3",name.Gb="b3",name.Rf="f5",name.Rb="b5",layout=slide .layout,gnames=slide.gnames) The shape of the file "slides.Rlayout" is : Block Column Row ID ID Name Control Missing Type Name Name Eurogentec 1 1 1 1 empty(1) empty OK PCR empty empty 1 2 1 2 empty(1) empty OK PCR empty empty 1 3 1 3 empty(2) empty OK PCR empty empty 1 4 1 4 empty(2) empty OK PCR empty empty 1 5 1 5 empty(3) empty OK PCR empty empty 1 6 1 6 empty(3) empty OK PCR empty empty 1 7 1 7 empty(4) empty OK PCR empty empty 1 8 1 8 empty(4) empty OK PCR empty empty 1 9 1 9 empty(5) empty OK PCR empty empty 1 10 1 10 empty(5) empty OK PCR empty empty 1 11 1 11 empty(6) empty OK PCR empty empty 1 12 1 12 empty(6) empty OK PCR empty empty 1 13 1 13 empty(7) empty OK PCR empty empty 1 14 1 14 empty(7) empty OK PCR empty empty 1 15 1 15 empty(8) empty OK PCR empty empty 1 16 1 16 empty(8) empty OK PCR empty empty 1 17 1 17 empty(9) empty OK PCR empty empty 1 18 1 18 empty(9) empty OK PCR empty empty 1 19 1 19 empty(10) empty OK PCR empty empty 1 20 1 20 empty(10) empty OK PCR empty empty 1 1 2 21 YEL039c gene OK oligo YEL039c YEL039c_OL 1 2 2 22 YEL039c gene OK oligo YEL039c YEL039c_OL 1 3 2 23 YPL187w gene OK oligo YPL187w YPL187w_OL The shape of the file "raw.csv" is : ID Name f5 b5 f3 b3 1 empty(1) NA NA NA NA 2 empty(1) NA NA NA NA 3 empty(2) NA NA NA NA 4 empty(2) NA NA NA NA 5 empty(3) NA NA NA NA 6 empty(3) NA NA NA NA 7 empty(4) NA NA NA NA 8 empty(4) NA NA NA NA 9 empty(5) NA NA NA NA 10 empty(5) NA NA NA NA 11 empty(6) NA NA NA NA 12 empty(6) NA NA NA NA 13 empty(7) NA NA NA NA 14 empty(7) NA NA NA NA 15 empty(8) NA NA NA NA 16 empty(8) NA NA NA NA 17 empty(9) NA NA NA NA 18 empty(9) NA NA NA NA 19 empty(10) NA NA NA NA 20 empty(10) NA NA NA NA 21 YEL039c 45258.207 2121.58444 49796.383 2194.7576 22 YEL039c 46875.83 2391.18833 60327.716 2335.1754 23 YPL187w 572333.812 1582.37666 876435.81 2054.3399 When I try to use the marrayPlots functions, for exemple : tmp=maImage(slide.raw,x="maGb",contours=T,bar=F) or maBoxplot(slide.raw,x="maPrintTip",y="maM") I've got the following message with the 1.7 and 1.8 versions of R : Error in m[, 1] : incorrect number of dimensions It's amazing because it works with the 1.6.2 version of R and old bioconductor packages. Does someone know how to handle this problem ? Thanks -- Patrice Godard Laboratoire de Physiologie Mol?culaire de la Cellule IBMM, Universit? Libre de Bruxelles rue des professeur Jeener et Brachet, 12 6041 Gosselies BELGIQUE tel. +32 2 650 99 60 fax. +32 2 650 99 50

sorry, it's not a problem of R version. The problem occurs when I put in my .Rprofile the following line : library(marrayClasses) library(marrayInput) library(marrayPlots) library(marrayNorm) It does'nt occur when I load these libraries manually at the begining of each R session. Le Mardi 20 Janvier 2004 11:44, Patrice Godard a ?crit : > Hi, > I'm using marray packages in order to normalize my data. > I load my data using the command lines : > slide.layout=read.marrayLayout("~/tmp/ > slides.Rlayout",ngr=8,ngc=4,nsr=20,nsc=20,ctl.col=6) > slide.gnames=read.marrayInfo("~/tmp/slides.Rlayout",info.id=6, labels=5) > slide.raw=read.marrayRaw("raw.csv",path="~/ > tmp/",name.Gf="f3",name.Gb="b3",name.Rf="f5",name.Rb="b5",layout=sli de.layo >ut,gnames=slide.gnames) > > The shape of the file "slides.Rlayout" is : > Block Column Row ID ID Name Control Missing Type Name Name Eurogentec > 1 1 1 1 empty(1) empty OK PCR empty empty > 1 2 1 2 empty(1) empty OK PCR empty empty > 1 3 1 3 empty(2) empty OK PCR empty empty > 1 4 1 4 empty(2) empty OK PCR empty empty > 1 5 1 5 empty(3) empty OK PCR empty empty > 1 6 1 6 empty(3) empty OK PCR empty empty > 1 7 1 7 empty(4) empty OK PCR empty empty > 1 8 1 8 empty(4) empty OK PCR empty empty > 1 9 1 9 empty(5) empty OK PCR empty empty > 1 10 1 10 empty(5) empty OK PCR empty empty > 1 11 1 11 empty(6) empty OK PCR empty empty > 1 12 1 12 empty(6) empty OK PCR empty empty > 1 13 1 13 empty(7) empty OK PCR empty empty > 1 14 1 14 empty(7) empty OK PCR empty empty > 1 15 1 15 empty(8) empty OK PCR empty empty > 1 16 1 16 empty(8) empty OK PCR empty empty > 1 17 1 17 empty(9) empty OK PCR empty empty > 1 18 1 18 empty(9) empty OK PCR empty empty > 1 19 1 19 empty(10) empty OK PCR empty empty > 1 20 1 20 empty(10) empty OK PCR empty empty > 1 1 2 21 YEL039c gene OK oligo YEL039c YEL039c_OL > 1 2 2 22 YEL039c gene OK oligo YEL039c YEL039c_OL > 1 3 2 23 YPL187w gene OK oligo YPL187w YPL187w_OL > > The shape of the file "raw.csv" is : > ID Name f5 b5 f3 b3 > 1 empty(1) NA NA NA NA > 2 empty(1) NA NA NA NA > 3 empty(2) NA NA NA NA > 4 empty(2) NA NA NA NA > 5 empty(3) NA NA NA NA > 6 empty(3) NA NA NA NA > 7 empty(4) NA NA NA NA > 8 empty(4) NA NA NA NA > 9 empty(5) NA NA NA NA > 10 empty(5) NA NA NA NA > 11 empty(6) NA NA NA NA > 12 empty(6) NA NA NA NA > 13 empty(7) NA NA NA NA > 14 empty(7) NA NA NA NA > 15 empty(8) NA NA NA NA > 16 empty(8) NA NA NA NA > 17 empty(9) NA NA NA NA > 18 empty(9) NA NA NA NA > 19 empty(10) NA NA NA NA > 20 empty(10) NA NA NA NA > 21 YEL039c 45258.207 2121.58444 49796.383 2194.7576 > 22 YEL039c 46875.83 2391.18833 60327.716 2335.1754 > 23 YPL187w 572333.812 1582.37666 876435.81 2054.3399 > > When I try to use the marrayPlots functions, for exemple : > tmp=maImage(slide.raw,x="maGb",contours=T,bar=F) > or > maBoxplot(slide.raw,x="maPrintTip",y="maM") > I've got the following message with the 1.7 and 1.8 versions of R : > Error in m[, 1] : incorrect number of dimensions > > It's amazing because it works with the 1.6.2 version of R and old > bioconductor packages. > > Does someone know how to handle this problem ? > Thanks -- Patrice Godard Laboratoire de Physiologie Mol?culaire de la Cellule IBMM, Universit? Libre de Bruxelles rue des professeur Jeener et Brachet, 12 6041 Gosselies BELGIQUE tel. +32 2 650 99 60 fax. +32 2 650 99 50