Dear Audrey,

thanks for your reply. I tried re-installing the package from bioc. It gave
the same results. I later installed 2.5 version of the software. This also
gave the same plots. There is still the same problem with ordering of
colors.
I see you asked me to use version 2.4.1 but I could not find it in the
release or development version. Am I looking at the wrong places? Please let
me know and thanks for your time...

Thank you
Lohith

P.S: I know this might be just a simple bug in the program and I wanted to
see if I can successfully tweak the R script for the software but I did not
find the R script in both the release and development versions..It would be
great to see the code..


On Thu, Oct 29, 2009 at 2:41 AM, Audrey Kauffmann <audrey@ebi.ac.uk> wrote:

> 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,
> Audrey
>
> 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
> EMBL - EBI
> Cambridge UK
> +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey
>
>

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