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There is no p-value associated with an expression estimate from RMA. It is a statistical method, so I guess in principle one could be computed using some type of resampling method but it is not currently available. I have looked at the difference between the MAS5 p-value and thresholding the RMA expression level at some low number like log(50) or log(32). The differences are fairly substantial. For that matter, the genes which are "significantly differentially expressed" also substantially differ with the normalization/summary method. --Naomi At 02:26 PM 8/22/2005, Devarajan, Karthik wrote: >Hello > >Does anyone have any experience comparing data quality (expression >estimates) between RMA and MAS5, in terms of Present/Absent calls? Also, is >there a way to obtain p-value associated with an expression estimate >directly from RMA? > >Thanks, >KD > > > > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111