[BioC] limma and print tip groups

[michael baron (IAH-P)]

Hi all,

I trawled a bit back through the archives and couldn't see an answer to this, so perhaps someone can help.

Limma uses a Printer Class to identify which print group a spot belongs to. This data object includes the number of grids, their arrangement and how many rows and columns of spots their are in each grid. This is easy to add to an RGList manually. The package does not seem to need a specific columns of info relating each spot to a particular grid, so I am guessing that there is an assumption that the functions are expecting the data to be arranged in a particular way. Is this so? I am analysing some data that is arranged in what I suspect is a non-standard way (all the spots in the first row across the ARRAY first, then the second row of the array, and so on). Is limma expecting the data to be 1st row of 1st grid, then 2nd row of 1st grid, and so on? If not, could someone tell me what it is expecting, or perhaps just that I am totally wrong and limma is working out the grid-spot linkage in some other way?

Thanks in advance,

Michael

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Michael D. Baron Ph.D.
Group Leader, Morbillivirus-Host Interactions
Institute for Animal Health
Ash Road,
Pirbright,
Surrey GU24 0NF
U.K.