[BioC] is-normalisation-really-required

[vijayaraj nagarajan]

dear friends
i have situation, where i thought its ok for me not to
do normalisation, i am afraid i may be wrong. i want
your advice in this regard.

we performed a wild type - mutant, dye-swap
experiment.
when we analysed the intensity values, they were
consistant among the two experiment (dye-swap). ie.,
almost same values for mutants in both the experiments
of the dye-swap.
since the values are almost same, i thought there
might not be any dye-bias, so i just went ahead,
averaged the two values, found out their ratio and
filtered genes with 2 fold change.

so i have done this without normalisation. 
i am afraid, i might be wrong, my 2 fold chaging genes
might be wrong...
kindly give me your advice in this regard.
i did analyse the data with limma, but the topTable
genes there never correlates with my 2 fold genes.

kindly correct me.
thanks

vijay
graduate student
department of biological sciences
the university of southern mississippi
MS, USA