Dave - 9 months ago 64

R Question

The code below runs t-test (un-paired) using 2 matrices as input and returns p-values but can someone show me the exact code needed to generate the p.adjusted values aka the

`FDR`

`m1 <-go_samp_matrix_data[grep(paste(input$mychooser2$left, collapse='|'), rownames(go_samp_matrix_data), ignore.case=TRUE),]`

m2 <-go_samp_matrix_data[grep(paste(input$mychooser2$right, collapse='|'), rownames(go_samp_matrix_data), ignore.case=TRUE),]

ttestmat1<-sapply(seq(ncol(m1)), function(x) f(m1[,x], m2[,x]))

f <- function(x,y){

test <- t.test(x,y, paired=FALSE)

out <- data.frame(pval = sprintf("%.3f", test$p.value))

return(out)

}

Answer Source

You need a vector of p-values, say `p.vect`

. Then you simply include that in `p.adjust()`

like so:

```
p.adjust(p.vect, "fdr")
```