[BioC] normalizeBetweenArrays gives an error

[Michael Nuhn]

Hi everyone!

I was hoping that someone here might have some insight on this problem:

I do normalization between arrays. For this I have written a little program
which creates an R/Bioconductor program which does this for me. It usually
works fine but now I have a set of GPR files where it fails. This is how it
goes:

First it loads the libraries:

library(marray)
library(convert)

Then it loads the GPR files:

files <- c("gpr_file__0", "gpr_file__1", "gpr_file__2")

Rf_label <- "F633 Median"
Rb_label <- "B633 Median"
Gf_label <- "F543 Median"
Gb_label <- "B543 Median"

g <- read.GenePix(files, name.Gf = Gf_label, name.Gb = Gb_label, name.Rf =
Rf_label, name.Rb = Rb_label)

A print tip-loess normalization for every slide:

gn <- maNorm(g, norm="p")

Then comes the normalization between arrays. I use the
"normalizeBetweenArrays" command here. I basically just copied the commands
from the book "Bioinformatics and Computational Biology Solutions Using R
and Bioconductor" on page 65:

gn at maW <- matrix(0,0,0)
gn.MA <- as(gn, "MAList")
g.nbta <- normalizeBetweenArrays(gn.MA, method="quantile")

This has always worked. But in this case I get the following message after
the second command:

> gn.MA <- as(gn, "MAList")
Error in "$<-.data.frame"(`*tmp*`, "Sub", value = c(TRUE, TRUE, TRUE,  :
 replacement has 7200 rows, data has 6912
Execution halted

This, at first glance rather puzzling message, seems to have something to do
with the "maSub" Slot of the GPR files. According to the docs, this field is
"indicating which spots are currently being considered." It is of type
boolean and 6912 values are set to TRUE and the others are FALSE. Huh? Why
aren't all spots being considered?

If I insert

maSub(gn)<-TRUE

before the command that fails, the normalization seems to work just fine.

However, I am wondering where the values from maSub come from and if it is a
good idea to just override them.

Does anybody know this?

Thanks in advance for hints,
Michael.

--
-----------------------------------------------------------
Dipl.-Inform. Michael Nuhn
Bioinformatik
Zentrum für Nanostrukturtechnologie und
Molekularbiologische Technologie

+49 (0)631 - 205 4334
nuhn at rhrk.uni-kl.de
http://nbc3.biologie.uni-kl.de/