justPLIER output log scale
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@andreas-heider-4538
Last seen 9.8 years ago
Dear bioconductor, I just asked myself if the values returned by justPLIER are log-base 2 oder 10? Can I change the base? What is the default? Thanks in advance, Andreas Heider [[alternative HTML version deleted]]
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@michal-okoniewski-2676
Last seen 10.2 years ago
Affy scanner produces values on two bytes 0-2^16, so if you have after the plier summarization values with whole-chip max around 13-15, then you have log2 - and they are used in such way as it is easier to interpret fold changes. Anyway - I think even the creators of plier gave it up and use RMA now :) Cheers, Michal On 5/9/11 3:58 PM, "Andreas Heider" <aheider at="" trm.uni-leipzig.de=""> wrote: >Dear bioconductor, >I just asked myself if the values returned by justPLIER are log-base 2 >oder >10? Can I change the base? What is the default? > >Thanks in advance, Andreas Heider > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
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So you say it is better to use RMA in any case? The literature I found is at best controversy :-D Andreas 2011/5/9 Michal Okoniewski <michal.okoniewski@fgcz.ethz.ch> > Affy scanner produces values on two bytes 0-2^16, so if you have after the > plier summarization values with whole-chip max around 13-15, then you have > log2 - and they are used in such way as it is easier to interpret fold > changes. > Anyway - I think even the creators of plier gave it up and use RMA now :) > Cheers, > Michal > > On 5/9/11 3:58 PM, "Andreas Heider" <aheider@trm.uni-leipzig.de> wrote: > > >Dear bioconductor, > >I just asked myself if the values returned by justPLIER are log- base 2 > >oder > >10? Can I change the base? What is the default? > > > >Thanks in advance, Andreas Heider > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@r-project.org > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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