[BioC] in-group missing arrayQualityMetrics()

[Wolfgang Huber]

Actually, it has been a deliberate design choice to not use more than 9 factor levels for colouring, to encourage users to group their levels beforehand if they want to use this functionality. It is hard to see how the kind of plots that arrayQualityMetrics makes could be useful with much larger numbers of colours. However, any suggestions are welcome!
	Wolfgang


On 8 Feb 2014, at 12:53, Wolfgang Huber <whuber at embl.de> wrote:
> Regarding the colours, please type
>  arrayQualityMetrics:::intgroupColors
> (in the R command line). You would have modify this function (e.g. in at arrayQualityMetrics source package) with a palette that has at least 12 colours. Any patches / suggestions here are welcome, and I’d be happy to insert them back into future versions of the package. As a work around, group the factor levels together so that there are <=9. Otherwise it may anyway be hard to distinguish them in the plots.
> 
> 	Wolfgang
> 
> 
> 
> On 7 Feb 2014, at 21:58, Kasoji, Manjula (NIH/NCI) [C] <manjula.kasoji at nih.gov> wrote:
>> I do have another question. I have a factor (grouping) that has 12 levels.
>> However only the first 9 are used. Is there a way to set the maximum to a
>> number higher than 9. For example this is the error and warning messages I
>> receive. Also, if you can explain what the error message means and how to
>> fix it that would be helpful.
>> 
>> The directory 'QC_Normalized_SampleID' has been created.
>> Error in UseMethod("xmlAttrs", node) :
>> no applicable method for 'xmlAttrs' applied to an object of class "NULL"
>> In addition: Warning messages:
>> 1: In maximumLevels(fac, n = length(colors)) :
>> A factor was provided with 12 levels, but only the first 9 were used for
>> coloring.
>> 2: In maximumLevels(fac, n = length(colors)) :
>> A factor was provided with 12 levels, but only the first 9 were used for
>> coloring.
>> KernSmooth 2.23 loaded