Thanks David. It seems not easy to compare multiple Matrices. karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? 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]]
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
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
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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
>
> ?__
> c/ /'_;~~~~kmezhoud
>(*) \(*) ????? ??????
>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.
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, ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? 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 > 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 <kmezhoud at gmail.com> > wrote: > >Thanks David. > >It seems not easy to compare multiple Matrices. > >karim > > > > ?__ > > c/ /'_;~~~~kmezhoud > >(*) \(*) ????? ?????? > >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. > >[[alternative HTML version deleted]]