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

[jeremy wilson]

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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