[Bioc-devel] Weird problem: invalid internal conversion?

[Groot, Philip de]

Hello all,

I bumped upon the following weird problem:

> coords <- rbind(c("-7.27996304796776", "-0.318763179006429"),
+                 c("-5.32491457041437", "0.0899675866959967"),
+                 c("-1.59446413449287", "-0.0537973666317704"),
+                 c("-4.07009809428656", "-0.311306729381296"),
+                 c("1.4145619288123", "0.212680197703627"))
> rownames(coords) <- c("A", "B", "C", "D", "E")
> colnames(coords) <- c("x", "y")
>
> Clusters <- as.factor(c(21, 18, 9, 23, 24))
>
> cbind(coords, Clusters)
  x                   y                     Clusters
A "-7.27996304796776" "-0.318763179006429"  "3"
B "-5.32491457041437" "0.0899675866959967"  "2"
C "-1.59446413449287" "-0.0537973666317704" "1"
D "-4.07009809428656" "-0.311306729381296"  "4"
E "1.4145619288123"   "0.212680197703627"   "5"
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
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
>

The column "Clusters" does not contain the numbers that I expect! Instead, it contains the references to
levels(Clusters)! I don't understand the reason. What do I miss here? Please note that this "feature" is at least present in R-2.10 and R-2.11 in both Windows and Linux. And yes: it is reproducible!

Regards,

Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>
Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>
             http://humannutrition.wur.nl/
             https://madmax.bioinformatics.nl/