Can someone provide me with a clear cut answer to the below:
Can I use the normalised .FPKM matrix file which feeds into EdgeR from RSEM abundance counts to annotate the top X amount of sequences unregulated/down-regulated between 2 conditions in Blast2goPro
I am reading FPKM values are unreliable....? What I am doing currently is working with the above mentioned normalised FPKM matrix file via Excel to filter out sequences present between conditions to try and group the sequences being up-regulated /down-regulated in respect to their GO mapping and annotations in Blast2go Pro. I work out fold change, then Log2 value. Would this be bullshit? Whilst I have wonderful heat maps generated by EdgeR to show diff. expression can I be confident in using the same FPKM values used to generate said heat maps for annotation analysis? Someone with a bit of knowledge in regards to this please help me.
I have used Trinity/ RSEM/EdgeR pipeline. Alternative methods are welcome but I'm needing somewhat speedy replies.
Any help appreciated.Thanks.