Dear Kasoji I think you want to follow the instructions on: http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMet rics.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 ?arrayQualityMetrics? 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 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 >>> >> >