Hi Mark, Thank you very much.
--Yiwen On Aug 9, 7:32 am, "Mark Robinson" <mrobin...@wehi.edu.au> wrote: > Hi Yiwen. > > I think this thread will answer your question in > detail:http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/... > > 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 -~----------~----~----~----~------~----~------~--~---
