[BioC] lty argument not recognised in plot function]

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Thu Sep 6 23:47:34 CEST 2007


Thank you! 
When will the update be available?
Will you also be able to change colours in plots also?  I am comparing
Illumina data to Affymetrix data so the similar I can make the outputs
the better! 

Also is it possible to compare Illumina data MA plots to a pseudo median
reference, rather than pairwise?
-----Original Message-----
From: Pan Du [mailto:dupan at northwestern.edu] 
Sent: Thursday, 6 September 2007 11:21 a.m.
To: Johnstone, Alice; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] lty argument not recognised in plot function]

Thanks for reporting the problem! Alice.
The current hist method in lumi package was not allowed to change lty
parameters. I have changed  the function and make it user changeable.

Pan Du


On 9/5/07 4:55 PM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:

> [BioC] lty argument not recognised in plot function
> Data: Wed, 5 Sep 2007 15:07:53 +1200
> Da: Johnstone, Alice <Alice.Johnstone at esr.cri.nz>
> A: <bioconductor at stat.math.ethz.ch>
> 
> Hi
> Trying to produce a histogram with the same line type for each sample 
> but it produces the error below:
> 
>> hist(data.lumi,col=cols,lty=1)
> Error in matplot(all.x, all.y, ylab = ylab, xlab = xlab, type = type,
:
> 
>    formal argument "lty" matched by multiple actual arguments
> 
> 
>> sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-08-11 r42469)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New 
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
methods
> 
> [8] base
> 
> other attached packages:
>   [1] lumiRatV1_1.3.0        lumi_1.3.29            annotate_1.15.3
> 
>   [4] AnnotationDbi_0.0.88   RSQLite_0.6-0          DBI_0.2-3
> 
>   [7] mgcv_1.3-25            affy_1.15.7
> preprocessCore_0.99.12
> [10] affyio_1.5.8           Biobase_1.15.26
> 
> 
> This has previously worked for me, so has something changed in the 
> devel package that I need to alter my script?
> Cheers
> Alice



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