We have two experiments run on illumina arrays done by the same company. I want to combine the data. I normally use Limmas functions (read.ilmn, and neqc) to deal with normalisation of the data. However if I combine these two experiments what is the best way of going about doing this. I am aware they need background correcting and quantile normalisation using the negative and positive control probes on the arrays.
edit - platform is the same, but need to compare healthy in one group with diseased in the other group. why it was done like this - well i didnt have any say in it - i cant go into that. the company we use is highly efficient and everything is standardised so batch should not be much of a problem.