[BioC] [TimeCourse Package] Warnings message

[Marcelo Luiz de Laia]

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