[BioC] images of affyPLM package in R 2.7.2

[Ben Bolstad]

As far as I a can recall no such changes have been made to this function
in the last several BioC releases. Additionally, testing this on my
machine is showing no such issues.

What chip type are you working with? Also your sessionInfo() don't show
the versions of affyPLM etc that you are using.

Ben

> library(affyPLM)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
> library(affydata)
> data(Dilution)
> Pset <- fitPLM(Dilution)
> image(Pset, which = 1, type = "resids",
+       col = pseudoPalette(low = "darkgreen",high = "red", mid =
"white"),
+       add.legend = TRUE)
> sessionInfo()
R version 2.7.2 (2008-08-25) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils
datasets 
[8] methods   base     

other attached packages:
[1] hgu95av2cdf_2.2.0    affydata_1.11.3      affyPLM_1.16.0      
[4] gcrma_2.12.1         matchprobes_1.12.0   affy_1.18.2         
[7] preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.1   












On Wed, 2008-09-10 at 09:35 -0400, Hui-Yi Chu wrote:
> Dear list,
> 
> I updated R from 2.6.2 to 2.7.2 recently but keep getting the error "figure
> margins too large" when plot pictures which never happened to me when using
> 2.6.2. Also, the legend disappears in R 2.7.2. After asking R mailing list,
> they think it's something specifically changed in image() of affy package,
> especially add.legend argument. But I dont know how to fix it or change the
> settings. Any suggestions are really appreciated!!!
> 
> ------------------------------
> library("affyPLM")
> aaa.qc <- fitPLM(aaa, background=T, normalize=T)       ## rma-normalized
> data
> image(aaa.qc, which = 1, type = "resids",
>       col = pseudoPalette(low = "darkgreen",high = "red", mid = "white"),
>       add.legend = TRUE)
> ------------------------------
> ps. aaa is an affybatch of raw data
> 
> I tried to add par(mar=c(2,2,2,2)) before the image line above to see if
> anything changed, but I still cannot see the legend which is visible in
> R2.6.2.
> 
> For more info, following is my two sessions of R.
> *1.*
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> *2.*
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> Thank you in advance!!
> Regards,
> Hui-Yi
> 
> 	[[alternative HTML version deleted]]
> 
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