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 and y group. I think I need to calculate a mean for each group, then use dist() function. I tried to find a R package to do it. 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 --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi! sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) --------------------------------------------------------------------- ______________________________________________ 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.
