Hi, I need to link ROSMAP TMT proteomics data round 2 to the individuals. Specifically, I want to merge table ROSMAP_Round2_Traits_FINAL.xlsx ([syn32835854](syn32835854)) with table ROSMAP_assay_proteomics_TMTquantitation_metadata.csv ([syn21323404](syn21323404)). I guess we should use "batch" and "channel" to merge (TMTdataSubmissionBatch = 2 only). But there is no batch or related column in ROSMAP_Round2_Traits_FINAL.xlsx ([syn32835854](syn32835854)), there is a column called "Plex", can anyone confirm that "Plex" is actually "Batch" in this table? Thanks!
Created by Li Sun rikku1983 Thank you both @abby.vanderlinden @edammer very much! Yes, 14 batches (plexes) with 16 TMT channels each in ROSMAP round 2 urea total homogenate proteomics is 224 total samples including 16 channels across the 224 dedicated to global internal standard (GIS, all sample equal mixture; 1-2/batch, for batch correction). Thus, there are 208 ROSMAP ProjIDs represented in the remaining channels of the 14 batches. Hi there, I think you're right that the "Plex" column in the traits excel spreadsheet can map to the "batch" column in the TMT assay metadata, since there are 14 batches and 14 plexes.
@edammer helped contribute this data -- Eric, can you confirm that "Plex" in the traits file is the same as "batch"?
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