Hi Yiwen. I think this thread will answer your question in detail: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1b0ab11fad9b4df3
In brief, the main difference is how the probe-level linear model is fit -- median polish OR iteratively reweighted least squares with a specified influence function. Note that in aroma.affymetrix, you have the 'flavor' argument in the RmaPlm and ExonRmaPlm objects. Cheers, Mark > > Hi, > > Following the "Reproducibility of other implementations Replication > test: RMA (background, normalization & summarization)" section in > aroma.affymetrix online document, I tried to compare the difference in > the RMA summary of gene expression index generated by > aroma.affymetrix, affyPLM and affy for a public dataset I am studying. > > I found that the RMA summary generated by aroma.affymetrix and affyPLM > (fitPLM) are highly consistent, while > the values between aroma.affymetrix/affyPLM and affy(rma function) are > quite different (Pearson correlation is only about ~0.97) and there is > a significant deviation from straight line in the scatter-plot. I was > wonder what is the main cause of the discrepency between RMA > calculated by aroma.affymetrix/affyPLM and affly(rma function). > > > Thanks a lot. > > Yiwen Chen > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
