[BioC] Normalizing data (that is not in microarray "format")
Emmanuel Levy
emmanuel.levy at gmail.com
Mon Dec 8 21:32:08 CET 2008
Dear Sean,
Thank you for your reply.
> Reading the help for normalize.loess, it appears that it takes a
> matrix as input. You do not need an affy object. Also, note that a
This is actually why I tried to use normalize.loess. Although I get
warnings, it does normalize my data.
The following piece of code generates the error mentioned in my previous email:
> my.mat = matrix(nrow=100, ncol=4, runif(400) )
> my.mat[1,1]=NA
> my.mat.n = normalize.loess(my.mat)
Warning messages:
1: In means[, j] + aux :
longer object length is not a multiple of shorter object length
I actually figured out that the NormalizeBetweenArray method from the
Limma package does the simple "scaling" normalization I was looking
for.
Best,
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] GOstats_2.4.0 Category_2.4.0 genefilter_1.22.0
[4] survival_2.34-1 RBGL_1.16.0 annotate_1.20.1
[7] xtable_1.5-4 GO.db_2.2.0 AnnotationDbi_1.2.2
[10] RSQLite_0.6-9 DBI_0.2-4 graph_1.18.0
[13] marray_1.20.0 limma_2.16.3 YEAST_2.0.1
[16] affy_1.20.0 Biobase_2.2.1
loaded via a namespace (and not attached):
[1] affyio_1.10.1 cluster_1.11.11 preprocessCore_1.4.0
> data.frame is not a matrix. For any of the normalization methods that
> you might choose, it helps to read the help carefully, as that will
> tell you what types of data can be used; most normalization routines
> will take a matrix as input. If you need more specific help, you will
> need to post some reproducible example code and give the output of
> sessionInfo().
>
> Sean
>
More information about the Bioconductor
mailing list