has specified data input has specified data output implements has format specification is executed in 'PLM' RMA R data frame 'affyPLM' http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. Nandini Badarinarayan affypdnn M-estimation regression Graph plot correction data normalization