I want to perform pairwise comparisons between the different groups. The output (heatmap) did not show any visible demarcation between the groups. Is there something wrong with my code? The input is raw RNA-seq count.

KIRP <- factor(clin.info$subtype, levels=c("1a", "1b", "1c", "2a", "2b", "2c","2d")) 
batch <- clin.info$admin.batch_number
design <- model.matrix(~0+KIRP+batch) 
rownames(design) <- rownames(clin.info) 

mrna.dge <- DGEList(counts=mat, group=KIRP, remove.zeros=T) 
keep <- filterByExpr(mrna.dge, design, min.count=50) 
mrna.dge <- mrna.dge[keep,,keep.lib.sizes=FALSE] 
mrna.dge <- calcNormFactors(mrna.dge)

v <- voom(mrna.dge, design, plot=TRUE) 
fit <- lmFit(v, design)
contrasts.matrix <- makeContrasts("KIRP1a-KIRP1b", "KIRP1a-KIRP1c","KIRP1a-KIRP2a", "KIRP1a-KIRP2b", "KIRP1a-KIRP2c", "KIRP1a-KIRP2d",
                                  "KIRP1b-KIRP1c","KIRP1b-KIRP2a", "KIRP1b-KIRP2b", "KIRP1b-KIRP2c", "KIRP1b-KIRP2d",
                                  "KIRP1c-KIRP2a","KIRP1c-KIRP2b", "KIRP1c-KIRP2c", "KIRP1c-KIRP2d",
                                  "KIRP2a-KIRP2b","KIRP2a-KIRP2c", "KIRP2a-KIRP2d",
                                  "KIRP2b-KIRP2c", "KIRP2b-KIRP2d",
                                  "KIRP2c-KIRP2d", 
                                  levels=design) 
fit2 <- contrasts.fit(fit, contrasts.matrix) 
efit <- eBayes(fit2)

Top DEGs

top.genes.all <- topTable(efit, number=Inf, adjust.method="BH", sort.by="F", p.value=0.05)

Input:

> dput(mat[1:10,1:10])
structure(c(999, 1009.61, 4077.44, 9350, 3401, 7964, 29, 46, 
38222, 6805, 536, 1569.99, 2000.28, 5853, 4190, 7052, 90, 33, 
11212, 11684, 2220, 2451.35, 3603.86, 8557, 7820, 9805, 22, 11, 
9827, 8669, 659, 2012.63, 1181.37, 4454, 2527, 7454, 23, 33, 
915, 13502, 790, 1869.43, 1522.12, 5264, 2777, 4450, 5, 26, 32164, 
5425, 1344, 5643.93, 1274.56, 14406, 6390, 13868, 4, 68, 400, 
20151, 1145, 2608.79, 4077.32, 11937, 2831, 14999, 17, 31, 859, 
9118, 1880, 1323.13, 7910.62, 16025, 11039, 16554, 11, 208, 8274, 
4014, 90, 535.66, 1835.07, 1239, 208, 2941, 19, 226, 4453, 3789, 
2140, 2365.18, 2375.95, 7034, 3195, 8222, 69, 319, 21306, 4883
), dim = c(10L, 10L), dimnames = list(c("ACE", "ACSM3", "ACTA2", 
"ACTR2", "ADAM10", "ADAR", "ADRA2B", "ADRA2C", "AEBP1", "AIFM1"
), c("TCGA.2K.A9WE.01", "TCGA.2Z.A9J1.01", "TCGA.2Z.A9J3.01", 
"TCGA.2Z.A9J6.01", "TCGA.2Z.A9J7.01", "TCGA.2Z.A9J8.01", "TCGA.2Z.A9JI.01", 
"TCGA.2Z.A9JJ.01", "TCGA.2Z.A9JQ.01", "TCGA.4A.A93W.01")))

> dput(clin.info[,c("survival", "subtype")][1:10,])
structure(list(survival = c("lts", "lts", "lts", "lts", "lts", 
"lts", "lts", "lts", "lts", "lts"), subtype = c("2a", "1a", "1a", 
"1a", "1b", "2b", "1a", "2a", "1a", "1c")), row.names = c("TCGA.Y8.A8S1.01", 
"TCGA.Y8.A8RZ.01", "TCGA.Y8.A8RY.01", "TCGA.Y8.A897.01", "TCGA.Y8.A896.01", 
"TCGA.Y8.A895.01", "TCGA.Y8.A894.01", "TCGA.WN.A9G9.01", "TCGA.V9.A7HT.01", 
"TCGA.UZ.A9Q0.01"), class = "data.frame")