[BioC] [TimeCourse Package] Warnings message

[Yu Chuan Tai]

Hi Marcelo,

Did you get any error when running mb.long() to get out1 and out2?
How do out1 and out2 look? Could you try plotProfile() without specifying
"pch" first and see what happens?

Yu Chuan
On Wed, 18 Jan 2006, Marcelo Luiz de Laia wrote:

> 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
>
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