Apparently limma_3.18.13 fixed the bug! Thanks again.


On Mar 28, 2014, at 4:54 PM, Yue Li <gorillayue@gmail.com> wrote:

> Thanks Jim. I am upgrading all of my installed bioc packages. It's likely to just be the transient bug from the old version of limma package like you mentioned.
> 
> 
> On Mar 28, 2014, at 4:51 PM, James W. MacDonald <jmacdon@uw.edu> wrote:
> 
>> Hi Yue,
>> 
>> Here is what I get:
>> 
>> > library(limma)
>> > png("tmp.png")
>> > MA <- new("MAList")
>> > MA$A <- runif(300,4,16)
>> > MA$M <- rt(300,df=3)
>> > status <- rep("Gene",300)
>> > status[1:3] <- "M=0"
>> > MA$M[1:3] <- 0
>> > status[4:6] <- "M=3"
>> > MA$M[4:6] <- 3
>> > status[7:9] <- "M=-3"
>> > MA$M[7:9] <- -3
>> > plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"))
>> > dev.off()
>> null device 
>>           1 
>> > png("tmp2.png")
>> > plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"), xlab="A")
>> > dev.off()
>> X11cairo 
>>        2 
>> > sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> 
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>> 
>> other attached packages:
>> [1] limma_3.18.13
>> 
>> And see attached. You have an outdated version of limma, so try updating.
>> 
>> Best,
>> 
>> Jim
>> 
>> 
>> 
>> On Fri, Mar 28, 2014 at 1:44 PM, Yue Li <gorillayue@gmail.com> wrote:
>> Hi Jim,
>> 
>> I tried it on both my Mac and Linux server and observed the same outcomes. Here are the session info.
>> 
>> Mac:
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> locale:
>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] limma_3.18.0
>> 
>> 
>> 
>> Linux:
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> 
>> locale:
>> [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>> [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>> [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=C
>> [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] BiocInstaller_1.12.0
>> 
>> 
>> 
>> On Mar 28, 2014, at 4:31 PM, James W. MacDonald <jmacdon@uw.edu> wrote:
>> 
>> > Hi Yue,
>> >
>> > I don't see that. Note that it is important to also include the output from sessionInfo() so people know which version of packages you are using. This may have been a transient bug that was already fixed.
>> >
>> > What is your sessionInfo()?
>> >
>> > Best,
>> >
>> > Jim
>> >
>> >
>> > On 3/28/2014 4:25 PM, Yue Li wrote:
>> >> Dear List,
>> >>
>> >> Somehow the plotMA function in limma package labels both x and y-axis title as 'M', where x-axis title should have been "A".
>> >>
>> >> The function resist the changes I try to make by setting the xlab in the plotMA function. See example below.
>> >>
>> >> I wonder if anyone came across the same thing and found an easy fix for this "bug".
>> >>
>> >> Thanks in advance,
>> >> Yue
>> >>
>> >> MA <- new("MAList")
>> >> MA$A <- runif(300,4,16)
>> >> MA$M <- rt(300,df=3)
>> >> status <- rep("Gene",300)
>> >> status[1:3] <- "M=0"
>> >> MA$M[1:3] <- 0
>> >> status[4:6] <- "M=3"
>> >> MA$M[4:6] <- 3
>> >> status[7:9] <- "M=-3"
>> >> MA$M[7:9] <- -3
>> >> plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"))
>> >>
>> >>
>> >> # same label
>> >> plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"), xlab="A")
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor@r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> > --
>> > James W. MacDonald, M.S.
>> > Biostatistician
>> > University of Washington
>> > Environmental and Occupational Health Sciences
>> > 4225 Roosevelt Way NE, # 100
>> > Seattle WA 98105-6099
>> >
>> 
>> 
>> <tmp.png><tmp2.png>
> 


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