I'm trying to find the differences between the test and control groups (genes). But the results are not consistence. For example, when there's a decrease in the test group, the fold change is positive! This happens in about 5/200 of them. Here's my codes, I don't know what's wrong... (because of the signed contact, I can't post any data here, sorry!) :
The data (df) is like:
gene Test1 Test2 Test3 Control1 Control2 Control3 Control4
A ...
B ...
C ...
...
n = 200
groups = factor(c(rep("test",3), rep("control",4)))
dge = DGEList(as.matrix(df), group = groups)
dge = calcNormFactors(dge, method = "TMM")
design_matrix = model.matrix(~0+groups, data = dge$samples)
colnames(design_matrix) = c("test", "control")
dge = estimateDisp(dge, design_matrix, robust=TRUE)
FIT = glmQLFit(dge, design_matrix, robust=TRUE)
model = glmQLFTest(FIT, contrast = makeContrasts(contrasts = c("test-control"), levels = design_matrix))
output = data.frame(Gene = rownames(dge$counts), FoldChange = 2^-(model$table$logFC))
thanks in advance!