I am currently working on brain transcriptome data of a male and female fish obtained using RNASeq. I wish to compare them and obtain the differentially expressed genes. All that I have got is a table containing the Transcripts per milllion (TPM) and the FPKM value for both the samples. I went through a few references which suggested to take log(fpkm) as the differential expression measure. However, I am interested in determining the statistical significance and determine the p-value and FDR of the differentially expressed genes. I learnt that few R packages like DESeq and EdgeR can do this job for me. Unfortunately, I am stuck up in using them as I understand that the TPM or FPKM values are not usable in those packages. Please can someone help me in sorting out this issue and let me know what is required to be done?
I am very much novice in this field and this is my first hands on with RNAseq data. Any help would be greatly appreciated.