I am trying to compare the RNA expression level of a specific gene in different cancer cell lines. Hence, I have downloaded several raw TPM data from EMBL, one from CCLE NIM groups and another one from Genetech. I am not an expert in this bioinformatic field, so I have some questions and I hope you can help me out.
the value of each data can be directly compared with each other? for example, the value of GAPDH in raw data from NIM groups, can I just directly compare the value with GAPDH in Genetech? or should I do another normalization?
For gene normalization, can I just directly normalize specific gene with the housekeeping gene by dividing the value? like MTOR/GAPDH.
Recently, I am trying to select some of the cell lines and targeted gene, trying to investigate gene expression among different cell line. I use the targeted gene divided by the housekeeping gene. In order to determine which cell lines consist of higher targeted mRNA level, I give the rank to calculated value between each cell line in different database and average the rank score. Is this making any sense or I shouldn't do it like this way?
Thanks for your help.
