[BioC] limma: merging RG list and normalisation

[Christopher Wilkinson]

I'd like to suggest a merge function for MAlists be implemented in limma, since
(I think) their are potential problems with the use of merge.RGlist and
print-tip normalisation of the merged RG list.

Within an experiment, I have slides spanning two print runs, in which spot
locations where changed between runs. Limma provides the merge function for
RGlist objects to allow merging data so that each row of the RGlist is the same
gene ie the rows of RG2 are rearranged to match the rows of RG1.

However when you come to doing print-tip normalisation, my understanding is
that
we really want the genes back in the original order, since the print-tip groups
are calculated by checking which row we are and how it fits into the layout
specifications. Otherwise we are doing print-tip normalisation on groups of
genes that are not in the same print-tip (for those that were re-arranged)

So I'd like to suggest that the merge function be implemented for MAlist
objects. Then when one has arrays from different print runs, you can read in
data from each print run into seperate RG objects, normalise them seperately,
then merge the normalised data together.

Cheers
Chris

Dr Chris Wilkinson

Research Officer (Bioinformatics)        | Visiting Research Fellow
Child Health Research Institute (CHRI)   | Microarray Analysis Group
7th floor, Clarence Rieger Building      | Room 121
Women's and Children's Hospital          | School of Applied Mathematics
72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005

Math's Office (Room 121)        Ph: 8303 3714
CHRI   Office (CR2 52A)         Ph: 8161 6363

Christopher.Wilkinson at adelaide.edu.au

http://mag.maths.adelaide.edu.au/crwilkinson.html