[BioC] [TimeCourse Package] Warnings message

[Marcelo Luiz de Laia]

Dear all!

I do an analysis under timecourse package and I receive a warning 
message after input a plot command.

plotProfile(out2,type="b",gnames=gnames,pch=c("R1","R2","R3","R4","R5","R6"),xlab="Tempo",ranking=3)
Warning message:
not using pch[2..] since pch[1] has multiple chars in: legend(legloc[1], 
legloc[2], legend = sort(unique(paste(object$con.group, 

What is the probable cause of this message?

I put the R-Script at the end of this message.

Our experiments was developed in this design:

- one bacterium was analysed in 4 times points. Each time point had 6 
biological replicate. We have been spotted 208 genes two times in the 
some slide. (timecourse package do not considere duplicate?!).

We apreciated all commentaries.

Thank you

+++++++++R-Script start+++++++++++
 library(timecourse)
 gnames <- scan("nameGENE.txt",what="character")
 assay <- rep(c("R1","R2","R3","R4","R5","R6"), each = 4)
 assay
 time.grp <- rep(c(1:4), 6)
 time.grp
 size <- rep(6,416)
 size
 todos <- read.matrix("todos_timecourse.txt",sep="\t")
 library(vsn)
 todos.norm <- vsn(todos)
 out1 <- mb.long(todos.norm,times=4,reps=size)
 out2 <- 
mb.long(todos.norm,times=4,reps=size,rep.grp=assay,time.grp=time.grp)
 plotProfile(out2,type="b",gnames=gnames,pch=c("R1","R2","R3","R4","R5","R6"),xlab="Tempo",ranking=1)
 plotProfile(out2,type="b",gnames=gnames,pch=c("R1","R2","R3","R4","R5","R6"),xlab="Tempo",ranking=2)
 plotProfile(out2,type="b",gnames=gnames,pch=c("R1","R2","R3","R4","R5","R6"),xlab="Tempo",ranking=3)

-- 
Marcelo Luiz de Laia
Ph.D Student in Genetics and Plant Breeding
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof.Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Fone: +55-016-3209-2675