[BioC] limma - arrays with different GAL files

[Helen Cattan]

Hi,
 
Can anyone help me with the following please?
 
I have an experiment using two sets of arrays with different layouts and
therefore different GAL files that I need to analyse together. A
previous suggestion on this mailing list was to normalize and then
combine the log ratios. Can anyone tell me what the code for combining 2
MALists is please?
 
Secondly one of the sets of arrays has the genes printed in duplicate
and the other set does not. Is there a way I can use dupcor.series for
the arrays with the duplicates and then combine them with the other set
of arrays? (or at least take the average - without having to manually
alter my gpr files)
 
Failing all this, if I just combined the MALists as they are, will I
have problems since the genes are in duplicate on some arrays with same
IDs etc and not others?
 
Finally....I have been told that the genes are the same on both types of
slides - whether this means 100% the same or more or less the same, I'm
not sure. If they are not completely identical how will the genes, that
are only on one set of arrays, be dealt with? i.e. will they be excluded
or will they be included in the calculations with data only from one set
of arrays?
 
Many thanks,
 
Helen
 

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