Entering edit mode
6.9 years ago
iza08.ik
▴
20
Hello,
I need help.
I wrote and used the code:
groups <- list(NDE = c(1,1), DE = c(2,1))
replicates <- c('adipose','brain')
CD <- new("countData", data = as.matrix(wang22)[1:1000,6:7], replicates = replicates, groups = groups)
libsizes(CD) <- getLibsizes(CD, estimationType = "quantile")
plotMA.CD(CD, samplesA = 'adipose', samplesB = 'brain', col = c(rep("red", 100), rep("black", 900)))
if(require("parallel")) cl <- makeCluster(8) else cl <- NULL
CD <- getPriors.NB(CD, samplesize = 10000, estimation = "QL", cl = cl)
CD <- getLikelihoods(CD, cl = cl, bootStraps = 3, verbose = FALSE)
topCounts(CD, group = "DE")
I don't know how to interpret the result and which gene are different expressed.
Can you help me, please?
