Hi Vivek, res1 <- read.table("positve-res1.txt",header=TRUE) ?dim(res1) #[1] 5292??? 4 #You could simplify the first loop as: mean_Res2 <- as.vector(rowMeans(res1)) ?identical(mean_Res1,mean_Res2) #[1] TRUE ##Regarding the second loop: pval_r2 <- as.vector(apply(res1,1,function(x) as.numeric(try(t.test(x)$p.value)))) length(pval_r2) #[1] 5292 ?sum(is.na(pval_r2)) #[1] 64 ##From running your second loop ?length(pval_r1) ##stopped at the first instance where data are essentially constant #[1] 63 ?res1[64,] #??????????? p118_diff p132_1_diff p132_2_diff mean #XLOC_000353???????? 1?????????? 1?????????? 1??? 1 ?head(which(is.na(pval_r2))) #[1]? 64? 78? 99 259 309 397 A.K. On Thursday, January 9, 2014 9:58 AM, Vivek Das <vd4mmind at gmail.com> wrote: I have some query. I would be glad if you can help me out. I am trying to calculate the p-value for a simple datafram, but am getting an error. The data in each column are relative differences.. The last column being the mean. I am giving the code snippet. I am not being able to figure out? why this error is coming up. My matrix looks like: mean_Res1<-c() for (i in 1:length(res1[,1])) { mean_Res1<-c(mean_Res1,mean(as.numeric(res1[i,]))) } pval_r1<-NULL for(i in 1:length(res1[,1])){ pval_r1<-c(pval_r1,t.test(as.numeric(res1[i,]))$p.value) print(i) } Error in t.test.default(as.numeric(res1[i, ])) : ? data are essentially constant I am not being able to figure out why is the t-test failing? Here is my matrix in the attachment. Can you suggest me? ---------------------------------------------------------- Vivek Das