[R] Overlapping Matrices By column correlation

[Karim Mezhoud]

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 <jdnewmil at 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:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
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> Sent from my phone. Please excuse my brevity.
>
> On January 9, 2015 7:57:02 AM PST, Karim Mezhoud <kmezhoud at 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
> ><dwinsemius at 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 at 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.
>
>

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