I have 5 data series(GSE). 4 from GEO database, 2 of which have the raw CEL files. I want to get all of this information into a single data matrix for analysis, using the RAW data where possible. I am very new to this whole area and it is proving difficult. Can anyone offer any help on this?
I can get a series into an expression set when using series matrix files via
gsexxxx= GEOquery("GSExxxx", GSEMAtrix=TRUE)- i think this is correct ?!
I think I can also get all cel files , normalise and into an expression set using ReadAffy function and gcRMA?
Any Help much appreciated, sorry if this question doesnt even make sense, as I said, I'm very new to it all!