[BioC] Is it normal that normalize.loess does not tolerate a single NA value?

[Emmanuel Levy]

Dear all,

I have been using normalize.loess and I get the following error
message when my matrix contains NA values:

> my.mat = matrix(nrow=100, ncol=4, runif(400) )
> my.mat[1,1]=NA
> my.mat.n = normalize.loess(my.mat, verbose=TRUE)
Done with 1 vs 2 in iteration 1
Done with 1 vs 3 in iteration 1
Done with 1 vs 4 in iteration 1
Done with 2 vs 3 in iteration 1
Done with 2 vs 4 in iteration 1
Done with 3 vs 4 in iteration 1
1 0.317319
Warning messages:
1: In means[, j] + aux :
 longer object length is not a multiple of shorter object length
2: In means[, k] - aux :
 longer object length is not a multiple of shorter object length
...

Is that normal? I'm scared that this introduces abnormalities in the
normalization.

Thanks for your help,

Emmanuel


> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] limma_2.16.3        GOstats_2.4.0       Category_2.4.0
 [4] genefilter_1.22.0   survival_2.34-1     RBGL_1.16.0
 [7] annotate_1.20.1     xtable_1.5-4        GO.db_2.2.0
[10] AnnotationDbi_1.2.2 RSQLite_0.6-9       DBI_0.2-4
[13] graph_1.18.0        YEAST_2.0.1         affy_1.20.0
[16] Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1        cluster_1.11.11      preprocessCore_1.4.0
[4] tcltk_2.8.0