This might be one of the trivial things but being new to RNA-seq data I am really confused on how to assign fpkm value for a gene in rna-seq data that has 3 or 4 isoforms.
I have downloaded analysed rna-seq data from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52450 and have noticed that transcripts belonging to the same gene(isoforms) have different fpkm values which is usual. But for my analysis purpose I am thinking whether It is ok if I sum up all the fpkm values of the isoforms to represent that particular gene's expression? or should I keep the values as it is?
genaA Isoform1 2.98
geneA isoform2 5.98
geneA isoform3 2.43
can i make it as geneA 11.39 (2.98+5.98+2.43)?