1 year ago

#180784

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JohnJ

Which statistical test in R to use to detect differential expression on a simulated dataset when there are three replicates

I was asked to begin this exercise in bioinformatics (https://uclouvain-cbio.github.io/WSBIM1322/sec-testing.html) by simulating a dataset of log2 fold-changes measured in triplicate for 1000 genes (abs function used to avoid negative logs)

sim <- abs(rnorm(3000, mean = 0, sd = 1))
simlog <- log2(sim)
simlog_mat <- matrix(simlog, ncol = 3,
       dimnames = list(paste0("gene", 1:1000), paste0("repl", 1:3)))

What statistical test should I use to test for 'differential expression'? The way the question is phrased, it seems I need to compare each replicate against the other? As there are 3 replicates I don't think I can use a t.test although the course material I'm using has only covered the ttest and FDR in this chapter.

r

matrix

simulation

hypothesis-test

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