Hi — I’ve recently been looking into the differential expression results from the ROSMAP TMT proteomics dataset and came across something I wanted to clarify. The AMP-AD Portal documentation (https://help.adknowledgeportal.org/apd/proteomics-data-and-methods) points to syn35221005 (`ROSMAP_DiffExp_TMTproteins.csv`) for the ROSMAP TMT differential expression results. These results also appear to be consistent with what is currently displayed on Agora. However, under the Agora folder, I also found syn32188234 (`Final_Agora_DE_TMT.csv`). For some of the genes we checked, the DE results in this file are substantially different from those in syn35221005. Could you clarify the relationship between these two files? In particular, is syn32188234 based on an older or different analysis pipeline/model, and should syn35221005 be considered the current/reference dataset for the TMT DE results displayed on Agora? Any additional context on why the results differ between the two files would be greatly appreciated. Thanks!

Created by Shaun Chen shaunfchen
Hello, Agora uses syn35221005 (`ROSMAP_DiffExp_TMTproteins.csv`) as its source data for the site, so I would use that file as ground truth. The other file appears to have been processed through a different pipeline as part of a [larger analysis relating neuropathology to proteomics](https://www.synapse.org/Synapse:syn27254960/wiki/616803). I'm not sure why it's in the Agora folder if it's not being used, but I would go with the file at syn35221005. I hope that helps, Jaclyn Beck

Two ROSMAP proteins DE results of TMT page is loading…