Hi, Please keep your replies on the R-help list so others may participate in the conversation.
On Thu, Sep 4, 2014 at 8:12 PM, Ding, Yuan Chun <ycd...@coh.org> wrote: > Hi Sarah, > > Thank you very much for your quick response. > > I checked the dist() function. It calculate distance between two samples with > a number of variables. > > Variable1 variable 2 variable 3 variable4 .... > X 3 5 6 7 > Y 4 8 9 10 > > So it is easy to calculate distance between x and y. > > But in my study, X is a group with 20 samples and y is another group with 30 > samples, so I need to calculate distance between x group between y group. That doesn't make any sense to me. If the variables are different, how can you calculate a distance between them? You also potentially run into scaling issues. Also, your original question (below) stated that your populations have 20 samples. > I think I need to get mean for each group, then use dist() function. I tried > to find a R package to do it. I think you'd be better off reconsidering what you're trying to accomplish. Sarah > Thanks, > > Ding > > -----Original Message----- > From: Sarah Goslee [mailto:sarah.gos...@gmail.com] > Sent: Thursday, September 04, 2014 4:49 PM > To: Ding, Yuan Chun > Cc: r-help@R-project.org > Subject: Re: [R] calculate Euclidean distances between populations in R with > this data structure > > I'd probably start with ?dist > > Sarah > > On Thu, Sep 4, 2014 at 4:10 PM, Ding, Yuan Chun <ycd...@coh.org> wrote: >> >> >> >> I want to calculate Euclidean distance between 12 populations, in each >> population there are 20 samples and each sample is measured for 100 genes >> (these are microarray data; the numbers here are just examples). >> The equation I found is: >> distance = sqrt{[sum(Average of xi -average of yi)^2] /n }, i=1 to n; >> where xi and yi are the expression of gene i over two populations with p and >> q samples (x1, x2,...,xp), (y1, y2,...,yq), n is the number of genes. >> part of data are pasted below >> row.names pop1.1 pop1.2 pop1.3 pop1.4 pop2.1 pop2.2 pop2.3 pop2.4 >> 7A5 5.38194 4.06191 4.88044 5.60383 6.23101 6.53738 4.80336 5.86136 >> A1BG 5.15155 4.29441 4.59131 4.90026 4.62908 4.48712 4.73039 4.46208 >> A1CF 4.22396 4.14451 4.41465 3.93179 4.89638 4.66109 4.20918 4.48107 >> A26C3 12.1969 12.4179 10.9786 11.7659 11.405 11.7594 11.1757 11.8128 >> How might one calculate these distances in R with this data structure? >> >> >> Thanks, >> >> Ding >> > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ R-help@r-project.org mailing list 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.