[BioC] Problem with marray

[Patrice Godard]

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 écrit :
> 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.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 Moléculaire de la Cellule
IBMM, Université 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