[R] Overlapping Matrices By column correlation

[Jeff Newmiller]

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.
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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]]
>
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