[BioC] marray, weights and normalizations..

Henning Redestig redestig at mpimp-golm.mpg.de
Mon Apr 18 12:14:16 CEST 2005


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

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