Count number of rows with a p-value equal to, or lower than 0.05

Question

I am new to R programming. I am facing issues which solving this:

Dataset:

set.seed(897)
ME <- matrix(rnorm(24000),nrow=1000)
colnames(ME) <- c(paste("A",1:12,sep=""),paste("B",1:12,sep=""))

Use apply() to calculate a statistical test for every row in ME. You want to ask whether the groups A and B are from the same population or from populations with different means. You can assume data to be normally distributed. Count the number of rows with a p-value equal to, or lower than 0.05.

I tried >P<- apply(ME , 1 , function(ME){ t.test(ME[1:1000])$p.value }) > length(which(P <= 0.05)) frown emoticon but this is incorrect

Yep , I tried it `P<- apply(ME , 1 , function(ME){ t.test(ME[1:1000])$p.value })` `length(which(P <= 0.05))` frown emoticon but this is incorrect — Rahul Saxena, Aug 30 '15 at 15:09
Please check the code in my solution. You are only passing single argument inside the `t.test`. Also, the `ME[1:1000]` is not correct as there are only 24 columns. So, within each row, the length is only 24. — akrun, Aug 30 '15 at 15:11

akrun · Accepted Answer · 2015-08-30T15:18:57.000

1

If the column names are not in a particular order, then we can use grep to find the index of column names that start with A and also with B.

 ind1 <- grep('^A', colnames(ME))
 ind2 <- grep('^B', colnames(ME))

Then we do the t.test by row using apply with MARGIN=1

 pval <- apply(ME, 1, FUN=function(x) t.test(x[ind1], x[ind2])$p.value)
 head(pval)
 #[1] 0.4987050 0.0303736 0.7143174 0.2955703 0.5082427 0.2109010

We get a logical index by comparing with 0.05

 v1 <- pval <= 0.05

Get the sum of the TRUE values to find the number of rows that have p.value less than 0.05

sum(v1)
#[1] 55

edited Aug 30 '15 at 15:18

answered Aug 30 '15 at 15:07

akrun

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Thanks @akrun , but in `pval <- apply(ME, 1, FUN=function(x) t.test(x[ind1], x[ind2])$p.value)` , In this I have to replace x with ME ? I am getting error when i tried to execute this command – Rahul Saxena Aug 30 '15 at 15:17
@andrahul Using the example you provided, I am not getting any error. Why you want to replace `x` with `ME`? – akrun Aug 30 '15 at 15:18
@andrahul Are you using the same example? What is the error message? – akrun Aug 30 '15 at 15:22
It was an error due to my workspace , i resolved that issue – Rahul Saxena Aug 30 '15 at 15:33
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Thanks for helping me out :) – Rahul Saxena Aug 30 '15 at 15:34
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@andrahul Thanks for the feedback. Glad to help you. – akrun Aug 30 '15 at 15:34

Count number of rows with a p-value equal to, or lower than 0.05

1 Answers1