Dear DR Jeff, OK! that is enough for me. There is no an alternative package that compares matrices as I want. Now I will develop one for me ;) Thanks,
Ô__ c/ /'_;~~~~kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Fri, Jan 9, 2015 at 5:29 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > Comparing anything requires some metric for comparison. Some metrics would > be very easy, others not so easy. For example, you could simply give your > mastic to the plot function to visually compare all columns. You are not > being clear about what you want, so it is your communication that is "not > so easy." > > You might find more domain-specific help in the Bioconductor help > forums... this mailing list focuses on using R assuming you know your > algorithm, not on suggesting algorithms. > --------------------------------------------------------------------------- > Jeff Newmiller The ..... ..... Go Live... > DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > --------------------------------------------------------------------------- > Sent from my phone. Please excuse my brevity. > > On January 9, 2015 7:57:02 AM PST, Karim Mezhoud <kmezh...@gmail.com> > wrote: > >Thanks David. > >It seems not easy to compare multiple Matrices. > >karim > > > > Ô__ > > c/ /'_;~~~~kmezhoud > >(*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ > >http://bioinformatics.tn/ > > > > > > > >On Thu, Jan 8, 2015 at 6:40 PM, David Winsemius > ><dwinsem...@comcast.net> > >wrote: > > > >> > >> On Jan 8, 2015, at 2:26 AM, Karim Mezhoud wrote: > >> > >> > Mantel test is interesting but it can't displays wish columns are > >> similar. > >> > > >> > Here an example: M > >> > gene1 gene2 gene3 gene4 gene5 > >> > Sample1 2 4 1 7 > > 2 > >> > Sample2 0 NA 2.3 1 9 > >> > Sample3 > >> > ...... > >> > > >> > M1, M2, M3 are three matrices of genes expression from three > >diseases. > >> > genes in columns and samples in rows. > >> > I would like to know which diseases has nearest gene expression > >profile > >> to > >> > others? and which genes are in common? > >> > >> Two things we need: > >> > >> 1) Reproducible example: Perhaps dput(list( M1[1:10,1:10) , M2[ > >1:10.1:10] > >> )) > >> > >> 2) A suggested metric for distance between such data objects that > >would be > >> acceptable to practitioners in whatever dark arts this activity is > >being > >> conducted > >> > >> > Any suggestion? > >> > Thanks > >> > Karim > >> > > >> > [[alternative HTML version deleted]] > >> > >> This is a plain text mailing list. > >> > >> > PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> > and provide commented, minimal, self-contained, reproducible code. > >> > >> -- > >> > >> David Winsemius > >> Alameda, CA, USA > >> > >> > > > > [[alternative HTML version deleted]] > > > >______________________________________________ > >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >https://stat.ethz.ch/mailman/listinfo/r-help > >PLEASE do read the posting guide > >http://www.R-project.org/posting-guide.html > >and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
