[BioC] query on variance parameters for RMA

Hugh Shanahan hugh at cs.rhul.ac.uk
Wed Feb 20 13:39:56 CET 2013


Hi,
      we would like to compute the parameters (i.e, the other parameters that are computed via the median polish algorithm) that are computed in the final summarisation step in RMA. In particular, we'd like to determine the parameter alpha_i that tells us how the estimate for the expression varies as a function of the probe. I guess it's possible to open up the relevant C-code and find it there, but are there are libraries that allow one to do it more easily ? I saw that affyPLM appears to be doing something similar - is this where we should be looking ? 

Many thanks,
Hugh



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