There are several methods to normalize data in the form of affyBatch objects. Some of these methods are: threestep, mas5calls, mascallsfilter, justMAS and rma.
Nevertheless, my data is in the data.frame format, as I have read my expression data from a .txt file. Can you please let me know what normalization and filtration methods can I use on a data.frame? Or is it possible to convert data.frame into an affyBatch object?
When I tried some of the normalization methods, I got the following error:
> dat.eset <- threestep(dat.fp,background.method="RMA.2",normalize.method="quantile",summary.method="median.polish") Error in threestep(dat, background.method = "RMA.2", normalize.method = "quantile", : argument is data.frame threestep requires AffyBatch > dat.mas5 <- mas5calls(dat) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mas5calls’ for signature ‘"data.frame"’