[BioC] [TimeCourse Package] Warnings message
Yu Chuan Tai
yuchuan at stat.Berkeley.EDU
Thu Jan 19 17:51:50 CET 2006
Hi Marcelo,
The warning was caused by the fact that you used more than 1 character for
the "pch" input argument for plotProfile(), which uses the same pch
argument from R's plot() function. According to the help file of
par(), pch can only be an integer or a single character:
"'pch' Either an integer specifying a symbol or a single character
to be used as the default in plotting points."
So if you change your pch argument to, for example, c("A","B","C"), then
the warning will disappear.
Yu Chuan
On Thu, 19 Jan 2006, Marcelo Luiz de Laia wrote:
> Dear Dr. Yu Chuan Tai,
>
> Thank you for prompt replay!
>
>
> Yu Chuan Tai wrote:
>
> >Did you get any error when running mb.long() to get out1 and out2?
> >
> >
>
> No!
>
> >How do out1 and out2 look?
> >
>
> > out1
> An object of class "MArrayTC"
> $M
> R1C T1R1T T3R1T T5R1T R2C T1R2T T3R2T T5R2T
> [1,] 6.677908 3.885578 5.215948 5.717402 6.767786 3.425970 5.464292 6.026186
> [2,] 6.598877 3.783673 5.052303 5.622144 6.967039 3.761490 5.627428 5.648088
> [3,] 1.334927 1.393307 1.418593 1.597419 2.112893 2.894773 2.298434 2.077417
> [4,] 1.917123 1.353949 1.408911 2.436594 1.859061 3.038671 2.143064 1.606409
> [5,] 2.218310 2.461884 2.265950 1.714568 1.274462 2.045000 1.636142 2.053304
> R3C T1R3T T3R3T T5R3T R4C T1R4T T3R4T T5R4T
> [1,] 6.616993 3.520077 5.609604 6.456539 6.770833 4.075315 7.143538 6.375819
> [2,] 6.544635 3.812006 5.684654 5.999495 6.978418 4.270595 7.211943 6.342325
> [3,] 1.290751 1.527019 2.490010 2.121042 2.483682 1.406305 1.691595 1.539216
> [4,] 1.890549 1.509971 2.341079 2.262312 1.992666 1.230446 1.753205 1.419647
> [5,] 2.117862 1.995821 2.116305 1.807638 1.203942 2.039304 2.099063 2.183528
> R5C T1R5T T3R5T T5R5T R6C T1R6T T3R6T T5R6T
> [1,] 6.844145 4.318939 6.655265 6.557516 6.663028 4.098101 7.169798 6.596244
> [2,] 7.056985 4.415535 6.803381 6.521790 6.645143 4.232166 6.954124 6.621673
> [3,] 2.100680 2.809253 1.951845 1.971931 1.339621 2.323106 1.306703 2.015207
> [4,] 2.140065 1.565866 2.391031 2.223658 1.488264 2.305137 2.096064 1.945653
> [5,] 1.636681 2.005430 2.050173 1.873903 2.236658 2.593845 1.686893 1.434244
> 411 more rows ...
>
> $prop
> [1] 0.02
>
> $nu
> [1] 5.4653
>
> $Lambda1
> [,1] [,2] [,3]
> [1,] 0.09284688 -0.02308453 -0.02261873
> [2,] -0.02308453 0.12974199 0.01222578
> [3,] -0.02261873 0.01222578 0.11376264
>
> $percent
> [,1] [,2]
> [1,] 6 52
>
> $size
> [1] 6 6 6 6 6
> 411 more elements ...
>
> $con.group
> [1] 1 1 1 1 1
> 19 more elements ...
>
> $rep.group
> [1] 1 1 1 1 2
> 19 more elements ...
>
> $time.group
> [1] 1 2 3 4 1
> 19 more elements ...
>
> $HotellingT2
> [1] 389.740926 404.656275 1.316475 1.056799 8.609435
> 411 more elements ...
>
> $pos.HotellingT2
> [1] 36 2 1 35 318
> 411 more elements ...
>
> > out2
> An object of class "MArrayTC"
> $M
> R1C T1R1T T3R1T T5R1T R2C T1R2T T3R2T T5R2T
> [1,] 6.677908 3.885578 5.215948 5.717402 6.767786 3.425970 5.464292 6.026186
> [2,] 6.598877 3.783673 5.052303 5.622144 6.967039 3.761490 5.627428 5.648088
> [3,] 1.334927 1.393307 1.418593 1.597419 2.112893 2.894773 2.298434 2.077417
> [4,] 1.917123 1.353949 1.408911 2.436594 1.859061 3.038671 2.143064 1.606409
> [5,] 2.218310 2.461884 2.265950 1.714568 1.274462 2.045000 1.636142 2.053304
> R3C T1R3T T3R3T T5R3T R4C T1R4T T3R4T T5R4T
> [1,] 6.616993 3.520077 5.609604 6.456539 6.770833 4.075315 7.143538 6.375819
> [2,] 6.544635 3.812006 5.684654 5.999495 6.978418 4.270595 7.211943 6.342325
> [3,] 1.290751 1.527019 2.490010 2.121042 2.483682 1.406305 1.691595 1.539216
> [4,] 1.890549 1.509971 2.341079 2.262312 1.992666 1.230446 1.753205 1.419647
> [5,] 2.117862 1.995821 2.116305 1.807638 1.203942 2.039304 2.099063 2.183528
> R5C T1R5T T3R5T T5R5T R6C T1R6T T3R6T T5R6T
> [1,] 6.844145 4.318939 6.655265 6.557516 6.663028 4.098101 7.169798 6.596244
> [2,] 7.056985 4.415535 6.803381 6.521790 6.645143 4.232166 6.954124 6.621673
> [3,] 2.100680 2.809253 1.951845 1.971931 1.339621 2.323106 1.306703 2.015207
> [4,] 2.140065 1.565866 2.391031 2.223658 1.488264 2.305137 2.096064 1.945653
> [5,] 1.636681 2.005430 2.050173 1.873903 2.236658 2.593845 1.686893 1.434244
> 411 more rows ...
>
> $prop
> [1] 0.02
>
> $nu
> [1] 5.4653
>
> $Lambda1
> [,1] [,2] [,3]
> [1,] 0.09284688 -0.02308453 -0.02261873
> [2,] -0.02308453 0.12974199 0.01222578
> [3,] -0.02261873 0.01222578 0.11376264
>
> $percent
> [,1] [,2]
> [1,] 6 52
>
> $size
> [1] 6 6 6 6 6
> 411 more elements ...
>
> $con.group
> [1] 1 1 1 1 1
> 19 more elements ...
>
> $rep.group
> [1] "R1" "R1" "R1" "R1" "R2"
> 19 more elements ...
>
> $time.group
> [1] 1 2 3 4 1
> 19 more elements ...
>
> $HotellingT2
> [1] 389.740926 404.656275 1.316475 1.056799 8.609435
> 411 more elements ...
>
> $pos.HotellingT2
> [1] 36 2 1 35 318
> 411 more elements ...
>
> > Could you try plotProfile() without specifying
> >"pch" first and see what happens?
> >
> >
>
> > plotProfile(out2,type="b",gnames=gnames,
> + xlab="Tempo",ranking=3)
> >
>
> >Yu Chuan
> >On Wed, 18 Jan 2006, Marcelo Luiz de Laia wrote:
> >
> >
> >
>
> Best whises
>
> Marcelo
>
> >>Dear all!
> >>
> >>I do an analysis under timecourse package and I receive a warning
> >>message after input a plot command.
> >>
> >>plotProfile(out2,type="b",gnames=gnames,pch=c("R1","R2","R3","R4","R5","R6"),xlab="Tempo",ranking=3)
> >>Warning message:
> >>not using pch[2..] since pch[1] has multiple chars in: legend(legloc[1],
> >>legloc[2], legend = sort(unique(paste(object$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
> >>
> >>_______________________________________________
> >>Bioconductor mailing list
> >>Bioconductor at stat.math.ethz.ch
> >>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
> >>
> >>
> >
> >
> >
>
>
> --
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
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