I am using DEseq package for my RNA SEQ samples so as to find differentially expressed genes between 2 samples
I have 2 RNA seq samples. One of them is CONTROL and the other sample is prepared by UV irradiation. Lets call the other sample as X.
Now since I don't have biological replicates in my case, I will have to use DEseq PACKAGE (working without any replicates section, http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf).
I randomly gave 2 conditions, "control" and "x" to my sample and I am looking for differentially expressed genes between 2 samples(up regulated or down regulated).
After following all the steps of DEseq at the last step where final results are to be computed
res <- nbinomTest(data,"control","x")
In the final output padj is always 1
padj - p-value adjusted for multiple testing using Benjamini-Hochberg to estimate the false discovery rate
Should I take into account only the pval column in my case or is there any other way to analyze this situation where I want to find differentially expressed genes between 2 samples(without biological replicates).