[BioC] limma, background correction and duplicate spots

[Helen Cattan]

Hi,
 
I am using limma for the first time and have a dataset that has some
negative values once the background has been subtracted from the spots.
These are in duplicate so I am using the dupcor.series method. This
works ok until I try and add in the backgroundCorrect method=minimum and
then I get the following error:
 
Error in array(val[["varBeta"]], c(rnkm1, rnkm1), list(namCoef,
namCoef)) : 
        length of dimnames[1] not equal to array extent
 
Firstly will it make any difference to the order of my differentially
expressed genes to perform some type of background correction, if so
what does the error message mean? and secondly what kind of values in
the top table am I looking for? The highest B value I have is -0.6
(without any background correction) which seems really low - is this any
good?
Any help is appreciated,
 
Helen
 
----- 
Helen Cattan <helen.cattan at jenner.ac.uk> 
Bioinformatics 
The Edward Jenner Institute for Vaccine Research 
Compton, Newbury, Berkshire, RG20 7NN UK 
Tel +44 (0)1635 577968 / Fax +44 (0)1635 577908 
 

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