Question: bitmap() extremely slow!
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gravatar for Groot, Philip de
8.1 years ago by
Groot, Philip de630 wrote:
Hello all, I run into the following problem. Regularly, I need to create affyPLM QC images as created by the affyPLM library and image(). I found out that in R-2.13.0 the creation of these images are very slow when I write them to bitmap(). Actually, I do use the function screenpng as provided by simpleaffy: function (file = "figure.png", width = 4, height = 4, res = 72) { bitmap(file = file, type = "png16m", width = width, height = height, res = res) } <environment: namespace:simpleaffy=""> > Creation of a single image takes more than 5 minutes whereas when I use the png() function (with res=72) the image is created within seconds! Why is bitmap() so slow? Changing type from png16m to png256 does not change a thing. Weird... > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affyPLM_1.28.5 preprocessCore_1.14.0 mogene11stv1cdf_2.3.0 [4] simpleaffy_2.28.0-1 gcrma_2.24.1 genefilter_1.34.0 [7] affy_1.30.0 Biobase_2.12.1 loaded via a namespace (and not attached): [1] affyio_1.20.0 annotate_1.30.0 AnnotationDbi_1.14.1 [4] Biostrings_2.20.0 DBI_0.2-5 IRanges_1.10.0 [7] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 [10] tools_2.13.0 xtable_1.5-6 > Regards, Dr. Philip de Groot Bioinformatician / Microarray analysis expert Wageningen University / TIFN Netherlands Nutrigenomics Center (NNC) Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: "De Valk" ("Erfelijkheidsleer"), Building 304, Verbindingsweg 4, 6703 HC Wageningen Room: 0052a T: 0317 485786 F: 0317 483342 E-mail: Philip.deGroot@wur.nl<mailto:philip.degroot@wur.nl> I: http://humannutrition.wur.nl<http: humannutrition.wur.nl=""/> https://madmax.bioinformatics.nl http://www.nutrigenomicsconsortium.nl<http: www.nutrigenom="" icsconsortium.nl=""/> [[alternative HTML version deleted]]
microarray affyplm • 435 views
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