[BioC] limma spacing: intra- and inter- block replicates

[Martin Kerick]

Dear all,

my array contains 4 replicates of each gene.
Each gene is present two times within one block
and this block is present two times on the array.

block structure:
XXXA
XXXB
XXXX

XXXA
XXXB
XXXX

Within block structure:

gkooooo
ooooooo
ooooooo
gkooooo
ooooooo
ooooooo


I think that within one block (2 of 4 replicates) the "evenly
spaced"-assumption holds true for all the genes. My question is, if the
"evenly spaced"-assumption can be applied also for replicates situated in
different blocks? I think it might work although there is a different
distance between the replicates from different blocks this difference is
entirely regular for all the genes.
If limma is applicable using all replicates as replicates I need to sort my
RGList so that spacing = 1 applies without loosing the ties between the
RG$genes attributes and the RG$R/RG$G intensity values.. do you have any
idea how to solve this computationally?

If the replicates in different blocks cant be treated as replicates one
could think of splitting the array into two arrays and calculating the
dupcor. series for each sub-array. If one gene pops up twice in the top
list, one would be more confident then..i think. Again one has to sort the
RGList according to RG$genes$ID and RG$genes$Block .. any hints how to solve
this problem ?

Many thanks in advance,

Martin