[BioC] marray, weights and normalizations..

[Henning Redestig]

Hi,

I am trying to use the Lapointe et al, PNAS 2004 data set from SMD 
consisting of 112 arrays. These are not as I understand it LIMMA 
compliant since the spots in the raw files are not directly in the 
spotting order (some spots have been left out) and therefore I decided 
to use the marray package which seem to be capable of handling even this 
kind of formatting.
Using read.SMD() to import the data seems to work and image() can plot 
the spots in spatial order indicating that the spotting order 
information has been kept.

Problem arise when I try to normalize the data using maNormMain() as I 
wish to weight the spots based on their flags. Setting w to the weights 
vector or NULL I get MA-plots as provided indicating a strong dependence 
between A and M in the lower intensity range when weights are used 
(lines are lowess fitted lines per print tip). Could anyone enlighten me 
as to why this is the case? Isnt the whole point of the normalization to 
remove any dependence between A and M?

The weights vector was set to 1 for flag=0, 0.1 for flag<=-50 and 0.01 
for flag<=-75 (GenePix flagging conventions, and weights chosen arbitrarily)

Very thankful for help