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Groot, Philip de
▴
630
@groot-philip-de-1307
Last seen 10.2 years ago
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=""/>
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