On Tue, May 11, 2010 at 8:46 PM, Saman Vaisipour <vaisipou@ualberta.ca>wrote: > Hi, > I have a question regarding the GDS2eSet function, I appreciate if you help > me with it. I am wondering whether this function does any kind of > normalization or not? Cause usually other functions that return eSet are > doing normalization, for example rma and mas5. > If GDS2eSet doesn't normalize then how can I normalize the resulting eSet > somehow that it becomes like a normal microarray dataset that I can use in > different experiments. > > Hi, Saman. The GDS2eSet does not attempt any normalization, as normalization is often platform- and experiment-specific. The data from GDS records is generally "normalized" at GEO, but that normalization can be quite variable as it is usually supplied by the submitter. For some purposes, it will be quite adequate to accept this normalization, but for others, the best option is to get raw data and start from scratch with quality control and normalization of those data. To normalize ExpressionSets, you can potentially do normalization of the matrix of values from a call to exprs()--as many normalization methods can be used with a matrix--and then replace that matrix with the "normalized" values. Again, the details of how to do that and to what extent it meets your needs will vary. Hope that helps, Sean [[alternative HTML version deleted]]