Dear All,

I am currently using an Agilent 4x44K model organism mosquito array for a one color time-course course experiment.  I am analyzing using the LIMMA package and have performed background correction and between array normalization as follows.

RoBb.corr <- backgroundCorrect(RoB, method="normexp", offset=16)

RoBb.corr.norm <- normalizeBetweenArrays(RoBb.corr, method="quantile")

However, after background correction the boxplot for a number of arrays become compressed (see example here: https://dl.dropbox.com/u/407047/Work/Catteruccia/minExample.html ).

I am not sure what is causing this compression although the quantile between array normalisation seems to correct for this….  However I am concerned about the possible affect on the data.  Has anyone else seen this compression with normexp correction?

I have read that background correction is not always optimal for Agilent arrays  (Zahurak et al.  2007 BMC Bioinformatics).


Do others routinely omit the background correction for Agilent arrays?

Best regards


Dr Sara Mitchell

Imperial College London

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