Hi, I want to search differential expressed genes in TCGA datasets by DEGseq. Below is my code:

geneExpMatrix1=readGeneExp(file="cancer.exprs.txt",geneCol=1,valCol=seq(2,414 ,1),header=T)

geneExpMatrix2=readGeneExp(file="normal.exprs.txt",geneCol=1,valCol=seq(2,20,1),header=T)

DEGexp(geneExpMatrix1=geneExpMatrix1,geneCol1=1,expCol1=seq(2,dim(cancer.exprs)[2],1),groupLabel1="tumor",geneExpMatrix2=geneExpMatrix2,geneCol2=1,expCol2=seq(2,dim(normal.exprs)[2],1),groupLabel2="normal",method="LRT",rawCount=TRUE,outputDir=paste(file1,".summary",sep=""))

The two files, cancer.exprs.txt and normal exprs.txt store the raw reads counts from cancer and normal samples. The genes is already filtered by median value of each gene (median>=5). The running of code report no mistake. However the up- and down-regulated genes vary in number. The number of up-regulated gene is over 10000 and the number of down-regulated genes is just about 30. I tried different method (MARS). It is the same! What`s wrong with me? Thanks