1 year ago
#180784
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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