[BioC] marray, weights and normalizations..

Gordon Smyth smyth at wehi.edu.au
Thu Apr 21 04:03:49 CEST 2005

>Date: Mon, 18 Apr 2005 12:13:03 +0200
>From: Henning Redestig <redestig at mpimp-golm.mpg.de>
>Subject: [BioC] marray, weights and normalizations..
>To: bioconductor at stat.math.ethz.ch
>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.

As far as I know, maNormMain() only handles spot weights on a single-array 
basis. I assume you are aware of that already.


>  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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