[BioC] ArrayQualityMetrics: Problem with labels in plots. A bug??

Audrey Kauffmann audrey at ebi.ac.uk
Thu Oct 29 10:41:39 CET 2009

Dear Jeremy,

Thank you for reporting this. You were right there was a problem in the 
code for the ordering of the colours.
I have now corrected it, so arrayQualityMetrics version 2.4.1 should be 
working fine.
Please let me know if you keep experiencing problems.

Best wishes,

jeremy wilson wrote:
> Dear BioConductors,
> I am using arrayQualityMetrics software package to do the QA. I very much
> like all the QA plots it produces including the latest PCA plot in one
> report. I am using the latest version of R(2.10) and BioC (2.5). I am facing
> a problem with inappropriate labeling of covariates. Please see the attached
> plots.
> I have total of 69 samples. I asked the software to label the plots based on
> a covariate, the summary of which is as below:
> Notation    total number of samples in order
> V                         23
> G                         38
> N                          8
> The problem is that it does not label the graphs correctly in the plots!! In
> the plots, the first set of samples correspond to V, the next 38 samples for
> G and the last 8 for N. In the boxplot for example, the G was labelled RED
> and this should correspond to 38 samples but in the plot, the boxplots
> corresponding to these 38 samples were colored GREEN. The ones that were
> labeled RED correspond to 8 'N' samples which should be represented in blue
> according to the label at the top of plot.  Likewise for the other two. I
> think it can be better understood at the first glance of the plots.
> The phenotype of the samples was given correctly.
> Following is the code I used for generating the aqm report.
> library(arrayQualityMetrics)
> arrayQualityMetrics(rat.ab, do.logtransform=TRUE, outdir="QA",
> intgroup="Material", grouprep=TRUE)
> I have attached only a few plots. I can produce all of them if it helps...
> It might take some time for the post to reach the mailing list as the
> earlier one I posted with a few more plots was held for moderator's approval
> as the size of the message body is over the limit!
> Please let me know what is wrong.
> Thanks in advance!
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Audrey Kauffmann
Cambridge UK
+44 (0) 1223 492 631 

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