[BioC] images of affyPLM package in R 2.7.2

[Henrik Bengtsson]

See the currently running r-help thread '"figure margins too large"
issue' started yesterday.  That seems to have a likely explanation for
the updates in R causing this; it seems that the default image
*dimensions* (not parameter 'mar') have changed.

My $.02

/Henrik

On Wed, Sep 10, 2008 at 7:21 AM, Ben Bolstad <bmb at bmbolstad.com> wrote:
> 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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>