I have noticed an issue with the limma normalizeWithinArrays function (and also with marray and maNorm). When normalizing two color data generated with an Agilent 20-bt scanner it fails to normalize the high intensity data (i.e. any points with an A value > 16). In our dataset we have in excess of 400 elements with red and green intensities ranging from 65500 to 475100. When we loess normalize the data any points beyond A=16 appear to be untouched by the normalization. If the attached figures come through this should be clear - when using maNorm and maPlot it will plot the loess line and you can see it stop at 16. Is it possible for loess normalization to be extended to this higher intensity data? Or am I just doing something wrong? If the attached plots come through they will make things clearer. Thanks, Peter Peter White, Ph.D. Director, Biomedical Genomics Core<http: genomics.nchresearch.org=""/> Research Assistant Professor of Pediatrics The Research Institute at Nationwide Children's Hospital and The Ohio State University > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils [8] methods base other attached packages: [1] convert_1.22.0 marray_1.24.0 oligo_1.10.3 [4] preprocessCore_1.8.0 oligoClasses_1.8.0 Biobase_2.6.1 [7] limma_3.2.2 svSocket_0.9-48 TinnR_1.0.3 [10] R2HTML_1.59-1 Hmisc_3.7-0 survival_2.35-8 loaded via a namespace (and not attached): [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.12 cluster_1.12.1 [5] DBI_0.2-5 grid_2.10.1 IRanges_1.4.13 lattice_0.18-3 [9] svMisc_0.9-56 tools_2.10.1 > -------------- next part -------------- A non-text attachment was scrubbed... Name: FoxD3 FoxD3_4 MvA Plots.png Type: image/png Size: 11628 bytes Desc: FoxD3 FoxD3_4 MvA Plots.png URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100311="" 2917a9a6="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: maPlot of normalized data.png Type: image/png Size: 9271 bytes Desc: maPlot of normalized data.png URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100311="" 2917a9a6="" attachment-0001.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: maPlot of raw data.png Type: image/png Size: 9268 bytes Desc: maPlot of raw data.png URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100311="" 2917a9a6="" attachment-0002.png="">