zhaoxiaofei
commented
1 year ago The corresponding author of the manuscript https://doi.org/10.1016/j.cell.2020.09.015 already answered my question on github at https://github.com/ParkerICI/tesla/issues/1 I will close this issue.
Please note that this is a question about the reproducibility of a research, so this is neither a bug report nor a feature request.
It looks like this package is able to compute all the four key statistics (i.e., binding affinity, agretopicity, foreignness, and tumor abundance) described in the paper entitled "Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction" (https://doi.org/10.1016/j.cell.2020.09.015) accurately with nearly 100% reproducibility except for tumor abundance.
I tried computing tumor abundance (in terms of TPM, transcript per million) using kallisto, and my result looks very different compared with the result posted at https://doi.org/10.1016/j.cell.2020.09.015 Table S4. I am wondering if you have any idea about such discrepancy?
I read the paper thoroughly and I did not find any detail about the computation of tumor abundance. I also tried contacting the corresponding authors of the paper, and unfortunately their email addresses are no longer valid.