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?
Any suggestion?
Thanks
Karim
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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
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]]