T-Test to every possible combination of samples

Asked Aug 23 '17 at 22:51

Active Aug 24 '17 at 18:13

Viewed 228 times

I'm new at R language, so I'm sorry if my question is too basic, but here we go...

I'm working with microarray analysis , utilizing the R software and right now I have to do a t-test to every possible combination of samples of my two analyzed groups.

It's basically a matrix of 20 columns of samples (10 for each group , condition 0 and condition 1) , and around 20000 rows of features (genes) . What I need is the p-value of all of those combinations.

example:

set.seed(777)
DataSample <- matrix(rnorm(10),nrow=20,ncol=10)
colnames(DataSample) <- c(paste("Condition 1",1:5,sep=" "),paste("Condition 
2",1:5,sep=" "))
DataSample

I'm looking for the p-values of Condition 1 1 x Condition 2 1, Condition 1 1 x Condition 2 2, Condition 1 1 x Condition 2 3...

Thank you !

edited Aug 24 '17 at 18:13

asked Aug 23 '17 at 22:51

Marcelo Falchetti

Have you looked at `combn()`? – Stedy Aug 23 '17 at 22:54
Hello, actually I have, but I don't know how to do a t-test using that command, and still get the p-values of all of those combinations for all the genes. Thank you for your attention ! – Marcelo Falchetti Aug 23 '17 at 23:01
1

Also look at `?pairwise.t.test`, which will allow you to adjust for doing a tonne of comparisons. – thelatemail Aug 23 '17 at 23:03
1

It should be pretty straight forward, I would suggest editing this question with an [mcve] so that myself and others can write better answers. – Stedy Aug 23 '17 at 23:04
I'll try to, sorry, I'm new to all of that, but I'll learn. – Marcelo Falchetti Aug 23 '17 at 23:07

T-Test to every possible combination of samples

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