based on an experimental design of testing 4 different substances("treatments") , dataset grows incrementally, as about on average a month period i get small batches of 5 CELs each(one control and 4 "treatments") which grow as beside the first batch, now i got the second batch which are "technical replicates" of the first batch. The platform is Affymetrix PrimeView(PM-only). So my main and very important question is:
as there is a "batch effect"(but on the same array batches) regarding the time of "creating" getting and each batch, should i preprossess each batch with the fRMA algorithm like this:
i.e. batch1 < ReadAffy(..)
norm1 <- frma(batch_1, background="rma", normalize="quantile", summarize="robust_weighted_average", target="probeset) ?
and then merge all the collected batches with some package such as inSilicoMerging which has a batch effect option ?
Or also there are other options in the frma() command that can also account for this ?
Please excuse me for my naive questions, but im a beginner in R, and i believe that this question is important, as in the end i want to unite these small batches i collect to have a final ExpressionSet