***********creating matrix and calculating variance across probesets******** x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y]) variableprobe<-apply(data.matrix[x,],1,var) hist(variableprobe) **************filter out low variance************* data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,] dim(data.sub) [1] 10000 140 summary(data.sub) a few samples: Sample_68_C Sample_69_D Sample_69_C Sample_70_D Sample_70_C Min. : 1.873 Min. : 1.893 Min. : 1.873 Min. : 1.722 Min. : 1.871 1st Qu.: 5.202 1st Qu.: 5.176 1st Qu.: 4.176 1st Qu.: 4.763 1st Qu.: 5.366 Median : 6.559 Median : 6.502 Median : 5.579 Median : 6.208 Median : 6.622 Mean : 6.473 Mean : 6.445 Mean : 5.697 Mean : 6.189 Mean : 6.558 3rd Qu.: 7.738 3rd Qu.: 7.742 3rd Qu.: 6.967 3rd Qu.: 7.547 3rd Qu.: 7.813 Max. :14.953 Max. :14.863 Max. :14.741 Max. :15.102 Max. :14.975 What is the best way to give me me probes only. I am trying to tell R to show me all the probes (10,000). What i want to do is to use the dist function to compute distances between the samples above. This function will take the matrix and computes the distances between the rows of the matrix. I tried dis <- dist(t(exprs(data.sub)), method="euclidean") but it is measuring the point by point which is too big. I would like to measure the distances between the rows. thanks!!! -- View this message in context: http://www.nabble.com/Calculating-the-Distance-tp15601307p15601307.html Sent from the R help mailing list archive at Nabble.com.