I am trying to perform cross platform normalization between affymetrix, illumina and agilent microarray data.
I know I can do it using Combat package which is now available in SVA package in R.
My problem is I have not recognized yet the structure of input files in SVA. The manual works with bladderbatch and phenodata that their structures is not clear.
I will appreciate any advice
Combat is used to attempt to remove unknown batch effects from single experiments, not to combine multiple experiments from different platforms. Combining data in the way you are after is not trivial, and people usually do this using meta-analysis. Just yesterday (I think) Jim MacDonald said he likes to use the GeneMeta package for this, so you might want to start there.