[BioC] in-group missing arrayQualityMetrics()

[Wolfgang Huber]

Dear Kasoji

I think you want to follow the instructions on:
http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html
i.e. run

source("http://bioconductor.org/biocLite.R")
biocLite("arrayQualityMetrics”)

Wolfgang

On 22 May 2014, at 17:41, Kasoji, Manjula (NIH/NCI) [C] <manjula.kasoji at nih.gov> wrote:

> Hi Wolfgang,
> 
> I hope you are doing well. I wanted to follow up with you regarding our
> last correspondence below about using the latest version of
> arrayQualityMetrics() (AQM) to be able to use the feature of handling 17
> colors. When I tried to update my version of AQM, it says that it is not
> compatible with my version of R. Please see the message below:
> 
>> install.packages("arrayQualityMetrics",type="source")
> Warning message:
> package ŒarrayQualityMetrics¹ is not available (for R version 3.0.2)
> 
> 
> Which version of R is the latest version of the package compatible with?
> 
> I appreciate your insight.
> 
> Regards,
> 
> Manjula
> 
> 
> On 2/8/14 7:14AM, "Wolfgang Huber" <whuber at embl.de> wrote:
> 
>> 
>> Version 3.19.6 (in svn, should be on the webpage in 1-2 days) now uses up
>> to 17 colours.
>> Ideally, of course, this should be user definable, but without making the
>> user interface more complicated.
>> 	Wolfgang
>> 
>> On 8 Feb 2014, at 12:58, Wolfgang Huber <whuber at embl.de> wrote:
>> 
>>> 
>>> 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 I¹d 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
>>> 
>> 
>