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.nutrigenomicsconsortium.nl/>




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