EdgeR, strange case (too many DEGs)

gistfile1.txt

###############
# mat_count: 60668 x 28 matrix, gene expression levels
# mat_count_rmlow: 18186 x 28 matrix
# group: A vector of factor: factor(rep(1:7, each=4))
###############

### Remove low-count genes and round count
is_lowgenes = rowMeans(mat_count) < 5
mat_count_rmlow <- mat_count[!is_lowgenes,]
dim(mat_count_rmlow)

x <- mat_count_rmlow
x <- round(x)

### Run EdgeR
y <- DGEList(counts=x, group=group) 
y <- calcNormFactors(y)

design <- model.matrix(~0+group)

y <- estimateDisp(y, design) # To estimate common dispersion and tagwise dispersions in one run (recommended) 
fit <- glmQLFit(y, design) 


###################
list_deg_comb <- list()

# 1: 1-3 vs. 4-5
vec = numeric(length(levels(group)))
vec[1:3] = 1
vec[4:5] = -1
res_comb1 <- glmQLFTest(fit, contrast = vec)
list_deg_comb[["1-3vs4-5"]] <- res_comb1


> nrow(topTags(list_deg_comb[["1-3vs4-5"]], n = Inf, p.value = 0.01))
[1] 18181
> nrow(topTags(list_deg_comb[["1-3vs4-5"]], n = Inf, p.value = 0.0001))
[1] 18181
> nrow(topTags(list_deg_comb[["1-3vs4-5"]], n = Inf, p.value = 0.000000001))
[1] 18180