[BioC] ArrayQualityMetrics: Grey boxes in boxplot

jeremy wilson jeremy.wilson88 at gmail.com
Thu Aug 12 18:51:33 CEST 2010

Dear Audrey,
thanks for your reply. The package is version 2.6 on R2.11. No, the
asterisks are not displayed in the html report even though they are
recognised as different from the rest by the package!
I have attached the outlier summary section screemshot for your reference.

Here is the sessionInfo

> sessionInfo()
R version 2.11.0 (2010-04-22)

 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arrayQualityMetrics_2.6.0 affyPLM_1.24.0
[3] preprocessCore_1.10.0     gcrma_2.20.0
[5] affy_1.26.1               Biobase_2.8.0

loaded via a namespace (and not attached):
 [1] affyio_1.16.0        annotate_1.26.0      AnnotationDbi_1.10.1
 [4] beadarray_1.16.0     Biostrings_2.16.5    DBI_0.2-5
 [7] genefilter_1.30.0    grid_2.11.0          hwriter_1.2
[10] IRanges_1.6.6        lattice_0.18-5       latticeExtra_0.6-11
[13] limma_3.4.3          marray_1.26.0        RColorBrewer_1.0-2
[16] RSQLite_0.9-1        simpleaffy_2.24.0    splines_2.11.0
[19] stats4_2.11.0        survival_2.35-8      tools_2.11.0
[22] vsn_3.16.0           xtable_1.5-6

Thank you

On Thu, Aug 12, 2010 at 3:25 AM, Audrey Kauffmann <ak.bergonie at gmail.com> wrote:
> Dear Jeremy,
> The grey boxes are the outliers as detected by the package (mean
> and/or IQR different from the others).
> They should correspond to the stars in the summary. Is that the case?
> Which version of arrayQualityMetrics are you using?
> Anyways, the outlier detection is here to help the user identifying
> array(s) different from the others but the interpretation remains
> yours. In this particular example, looking at the boxplots before and
> after normalisation the arrays 1, 5, 8  and 9 seem fine to me.
> Best wishes,
> Audrey
> 2010/8/11 jeremy wilson <jeremy.wilson88 at gmail.com>:
>> Dear all,
>> I am noticing that some of my boxes in the boxplot are colored grey. I
>> looked at the code to plot the boxplots (aqm.boxplot) and observed
>> that there is a parameter "outlier" whose length if not zero  will
>> color the respective arrays as grey. These outliers as I understand
>> from the code are a union of outliers based on mean and variance of
>> intensity distributions. Just by looking at the boxplots (attached), I
>> do not think the 1st and the 5th arrays are outliers?
>> The thing is that these were not shown as outliers in the report with
>> a * mark in the before normalization report. The 9th array which is
>> shown as grey in the after normalization plot was shown as outlier (*)
>> when the eset after normalization was used to perform AQM.
>> Are the grey colored ones really outliers or some thing else? If they
>> are outliers, why are the three arrays from the before normalization
>> boxplot not marked as outliers in the report?
>> Please let me know
>> Thank you
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> --
> Audrey Kauffmann
> Bergonie Cancer Institute
> 229 Cours de l'Argonne
> 33076 Bordeaux
> France
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