I have four RNA-seq data from four different samples. Actually I am handling the plant transcriptome data of one control and one treatment for each 2 differential conditions. They have no replicates. So FPKM was calculated for normalization. I want to do DGE between them. I know from another post Gordon suggested that: If FPKM is really all you have, then convert the values to a log2 scale (y = log2(FPKM+0.1) say) and do an ordinary limma analysis as you would for microarray data, using eBayes() with trend=TRUE. Do not use voom, do not use edgeR, do not use DESeq. (Do not pass go and do not collect $200.) This isn't 100% ideal, but is probably the best analysis available.
But It doesn't work for me without replicates. Could you give me an idea to do DGE for this condition? I know It is not ideal without replicates but there is no way for now!