[BioC] arrayQualityMetrics

[audrey]

Hi Al,

Nice suggestion, I am still looking for a nice way to present these 
density plots with the names. So I will think about it with your suggestion.

Cheers,
Audrey

Al Ivens wrote:
> Hi Audrey,
>
> Thanks for the prompt reply.  I take your point about split.plots,
> although sometimes it IS useful to see everything together!  Could the
> html report perhaps have a separate graphic with the legend, which might
> thus get around the "space on the plot" issue?
>
> Cheers and thanks,
>
> a
>
>   
>> -----Original Message-----
>> From: audrey [mailto:audrey at ebi.ac.uk] 
>> Sent: 19 December 2007 09:03
>> To: Al Ivens
>> Cc: 'bioc'
>> Subject: Re: [BioC] arrayQualityMetrics
>>
>>
>> Hi Al,
>>
>> Thank you for the useful feedback. In the development version of 
>> arrayQualityMetrics, I have added a legend with the name of the 
>> experiments on the density and ecdf plots. I will think about 
>> adding the 
>> same on the RNAdeg plot in the next version.
>> However when there are too many experiments there is not 
>> enough place on 
>> the plot to write all the experiment names so I advice you in 
>> that case 
>> to use the argument "split.plots" of arrayQualityMetrics and 
>> to set it 
>> at 20 maximum.
>>
>> Thank you,
>> Audrey
>>
>>
>> Al Ivens wrote:
>>     
>>> Hi,
>>>
>>> I have been using arrayQualityMetrics, and find it very useful. 
>>> However, to make it even more useful, would it be possible to have 
>>> legends for some of the plots, e.g. density/ecdf, RNAdeg 
>>>       
>> incorporated 
>>     
>>> in the output?
>>>
>>> Cheers and thanks,
>>>
>>> a
>>>
>>>
>>>   
>>>       
>>>> sessionInfo()
>>>>     
>>>>         
>>> R version 2.6.0 (2007-10-03)
>>> i386-pc-mingw32 
>>>
>>> locale:
>>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>>> Kingdom.1252;LC_MONETARY=English_United
>>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>>>
>>> attached base packages:
>>>  [1] grid      splines   tools     stats     graphics  
>>>       
>> grDevices utils
>>     
>>> datasets  methods   base     
>>>
>>> other attached packages:
>>>  [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1        CCl4_1.0.6
>>> simpleaffy_2.14.05       
>>>  [5] affyPLM_1.14.0            gcrma_2.10.0
>>> matchprobes_1.10.0        RColorBrewer_1.0-2       
>>>  [9] vsn_3.2.1                 limma_2.12.0              affy_1.16.0
>>> preprocessCore_1.0.0     
>>> [13] affyio_1.6.1              genefilter_1.16.0         
>>>       
>> survival_2.34
>>     
>>> geneplotter_1.16.0       
>>> [17] lattice_0.17-2            annotate_1.16.1           
>>>       
>> xtable_1.5-2
>>     
>>> AnnotationDbi_1.0.6      
>>> [21] RSQLite_0.6-4             DBI_0.2-4                 
>>>       
>> Biobase_1.16.1
>>     
>>> loaded via a namespace (and not attached):
>>> [1] KernSmooth_2.22-21
>>>   
>>>
>>>
>>>
>>>
>>>   
>>>       
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