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t-test for microarray analysis in R

HI, I have a code , I dont know if the code exactly falls for paired t test or not? 

logX.cl <- c(0, 0, 1,1)
ttest = function(x) {
  tt = t.test(x[logX.cl == 0], x[logX.cl == 1])
  return(c(tt$statistic, tt$p.value))
}
r
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updated by Biostar Biostar • written by gladnovin • gladnovin

No, look here: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/t.test.html

t.test(..., ..., paired=TRUE)

In this example, though, you are literally just comparing 2 values versus 2 values - makes no sense (?). Whatever is in the object x, you will only be taking index 1-4 from it.

Can you please explain what you are aiming to do? For microarray data, the common (and I would say standardised, at this stage) method to use is limma: https://bioconductor.org/packages/release/bioc/html/limma.html

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written by Kevin Blighe Kevin Blighe

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