[BioC] NormalizeBetweenArrays

[Jason Skelton]

Hi  Gordon and everyone

i'm using (Limma V1.5.1, R V1.8.0)

I have an experiment with seven treatments as outlined below

   Germball Cerc TwoDay SevenDay TwentyOneDay AdultWorm Egg
1        -1    0      0        0            0         0   0
2        -1    0      0        0            0         0   0
3        -1    0      0        0            0         0   0
4         1    0      0        0            0         0   0
5         0   -1      0        0            0         0   0
6         0   -1      0        0            0         0   0
7         0   -1      0        0            0         0   0
8         0    1      0        0            0         0   0
9         0    0     -1        0            0         0   0
10        0    0     -1        0            0         0   0
11        0    0     -1        0            0         0   0
12        0    0      1        0            0         0   0
13        0    0      0        1            0         0   0
14        0    0      0       -1            0         0   0
15        0    0      0       -1            0         0   0
16        0    0      0       -1            0         0   0
17        0    0      0        0           -1         0   0
18        0    0      0        0           -1         0   0
19        0    0      0        0           -1         0   0
20        0    0      0        0            1         0   0
21        0    0      0        0            0         1   0
22        0    0      0        0            0        -1   0
23        0    0      0        0            0        -1   0
24        0    0      0        0            0        -1   0
25        0    0      0        0            0         0  -1
26        0    0      0        0            0         0  -1

I'm currently using normalizeWithinArrays for each of the 26 slides and 
treating them completely seperately
then liner model fitting ->  classifyTests etc................

However I'd like to normalize within treatments

Is there an easy way of taking the normalized *within* arrays results
and *normalizing between arrays* for each treatment seperately then 
combining these back in to a complete MAlist ?
for use in further downstream analysis to compare treatments using 
ClassifyTests etc ?

Many thanks

J.



-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919