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) x86_64-pc-linux-gnu locale: [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 [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=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 > -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot-1.png Type: image/png Size: 32527 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100812="" 0c985617="" attachment.png="">