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Hi Ingrid, We are working on updating the docs within the package - at the moment, the best source of information about Plier is at the Affymetrix website. The parameter names in the function should translate relatively easily to the Affy documentation. Regards, Crispin On 14/11/07 14:50, "Ingrid H. G. ?stensen" <ingrid.h.g.ostensen at="" rr-research.no=""> wrote: > Hi > > Does it exist any documentation on how to use the plier package? > > Regards, > Ingrid > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}

Hello, In fact, I looked at this in the past, and I found that the parameters do not translate all that well... The "Guide to Probe Logarithmic Intensity Error (PLIER) Estimation" from Affymetrix web site mentions four types of normalization: PM-MM, PM-B, PM Only, and "MM treated as additional PM". Function justPlier() in Bioconductor has on the other hand 'separate', 'pmonly', 'mmonly', and 'together'. What is the relationship? The function also has a whole bunch of parameters that Affy documentation doesn't elude to directly. This is in sharp contrast to algorithms like RMA that have only a few parameters that are easy to understand. A better explanation would be most welcome... I think this may be causing justPlier() more problems on the psychological level of users. I've heard statisticians saying that they won't use it because they are uncertain of what it really does, since it doesn't map in a straightforward way to the algorithm description provided by Affy. And there is no way of knowing how to call it so that it performs calculations akin to the ones mentioned in Affy's documentation. Best, Michal Blazejczyk FlexArray Lead Developer http://genomequebec.mcgill.ca/FlexArray/ > Hi Ingrid, > We are working on updating the docs within the package - at the moment, the > best source of information about Plier is at the Affymetrix website. The > parameter names in the function should translate relatively easily to the > Affy documentation. > Regards, > Crispin > On 14/11/07 14:50, "Ingrid H. G. ?stensen" > <ingrid.h.g.ostensen at="" rr-research.no=""> wrote: >> Hi >> >> Does it exist any documentation on how to use the plier package? >> >> Regards, >> Ingrid