Hi I am new to the field and I am currently stuck on deciding how to deal with different Transcription ID of a given Gene ID.
I have a data sheet containing FPKM values from RNAseq analysis of mouse cancer cell line grown in different conditions (4 samples) and I want to compare the gene expression values across the samples.
In the data file I have, most genes have several different transcript Ids and from my understanding is that a given gene can be transcribed into several different proteins due to alternative splicing, and the resulting proteins may or may not have the same function from one another.
If I want to compare the expression level of a gene across the 4 samples, would it be logical to add all the FPKM values of each different transcription ID of a given gene and compare the sum value to different samples or would it be a better choice to leave the FPKM values separately for each transcriptions?
I'm not sure if I explained my situation clearly enough but I would appreciate any input on the matter
Thank you in advance!