EBseq manual recommends heatmap for DE visualisation.

heatmap.2(NormalizedMatrix[GenesOfInterest,], scale="row", trace="none", Colv=F)

The normalized matrix may be obtained from GetNormalizedMat() function.

Can someone explain, what is the "[GenesOfInterest]" here.. Is it a file containing list of differentially expressed genes?

Given how it is written I would think that it is subsetting the matrix to keep only genes that are of interested. Subsetting matrices in R is done with the syntax matrix[rows, columns], if 'rows' or 'columns' are left empty all rows/columns are returned. It could hence be a vector with True/False values or a numeric vector with the row numbers corresponding to the genes of interested. If your 'NormalizedMatrix' has row names it could also be a vector with names that you would like to generate a heatmap for.

Yes, my 'NormalizedMatrix' has row names.
These are my files:
The count matrix from RSEM is "Rsemcount"

"671H.genes.results" "86302H.genes.results" "11015D.genes.results""671D.genes.results" "86302D.genes.results"
"GFHJ01000001.1" 0.00 0.00 0.00 0.00 0.00
"GFHJ01000002.1" 2.00 4.00 1.00 9.00 1.00
"GFHJ01000003.1" 0.00 0.00 0.00 0.00 1.00
"GFHJ01000004.1" 1.00 19.00 2.00 17.00 0.00
"GFHJ01000005.1" 0.00 0.00 0.00 0.00 0.00
"GFHJ01000006.1" 1.00 7.00 0.00 3.00 0.00

I did the following in R:

In=read.table("Rsemcount", stringsAsFactors = F, row.names= 1, header = T) Data=data.matrix(In)
sizes=MedianNorm(Data) NormData=GetNormalizedMat(Data,sizes)

head(NormData)
X671H.genes.results X86302H.genes.results X11015D.genes.results X671D.genes.results GFHJ01000001.1 0.000000 0.000000 0.000000 0.0000000
GFHJ01000002.1 3.462638 1.574628 2.914371 2.2445692
GFHJ01000003.1 0.000000 0.000000 0.000000 0.0000000
GFHJ01000004.1 1.731319 7.479485 5.828742 4.2397418
GFHJ01000005.1 0.000000 0.000000 0.000000 0.0000000
GFHJ01000006.1 1.731319 2.755600 0.000000 0.7481897
X86302D.genes.results
GFHJ01000001.1 0.000000
GFHJ01000002.1 1.736781
GFHJ01000003.1 1.736781

I have combined the list of DE genes for 3 treatments in file combineddelist
head combineddelist
GFHJ01002875.1
GFHJ01004450.1
GFHJ01004863.1
GFHJ01004888.1
GFHJ01004990.1
GFHJ01005067.1

GenesOfInterest=read.table("combineddelist", stringsAsFactors = F, header = F)

GenesOfInterest
V1
1 GFHJ01002875.1
2 GFHJ01004450.1
3 GFHJ01004863.1
4 GFHJ01004888.1
5 GFHJ01004990.1
6 GFHJ01005067.1
7 GFHJ01005131.1

heatmap.2(NormData[GenesOfInterest,], scale="row", trace="none", Colv=F)
Error in NormData[GenesOfInterest, ] : invalid subscript type 'list'

I tried read.list to read the DE genes list but the function is not found. I am new to RNASeq and R. Please, help me how to use row names as vectors for my DE gene list.