Hello,
May I know where can I find the trait file for round 1? syn32539359
Thanks,
Jenny Empawi
Created by Jenny Empawi jaempawi Hi Yang and Jenny, these are good questions. I'm hopeful someone from the Emory team can help answer --
@dduong or @nseyfried, can you please advise on which files from the ROSMAP Round 2 proteomics to use for downstream analysis, and where we can find them? If there are any missing let me know and we can get them uploaded to the AD Portal!
Thanks,
Abby Hello @jaempawi @abby.vanderlinden,
Thanks for the useful discussion. I am wondering if these problems resolved. I am also looking for:
1) ROSMAP TAMPOR batch-corrected protein matrix for round 1.
2) The same QCed protein matrix for round 2. (I can see under syn26051783, there are protein matrix, but I couldn't find corresponding QC-ed files like for Round 1)
I guess the general question is which file and which protein value should be used for downstream analysis. For Round 1, I can see in the file syn21971722, or even under search_ouput, the file syn21241539, both contain normalized abundance. I might missed something but here is no README to explain the column name.
Any suggestions or updates would be much appreciated.
Sincerely,
Yang
Hello Abby,
For ROSMAP, is there TAMPOR batch-corrected protein matrix? I found out that syn21266454 is not the cleanDat but it is similar to Naive log2(abundance/GIS*Cross-protein relative abun) plot. Too bad I couldn't upload my PCA plot here.
Thank you for your help!
Best,
Jenny Empawi Oh no, that's a good catch! I'm not sure where the matrix is, but hopefully the Emory team will know.
@ductyler do you know where the protein counts matrix is for the ROSMAP Round 2 TMT data? It looks like it never got uploaded in the public AD Portal project with the rest of the files. Hello Abby,
Thank you for the information. May I know where can I find raw and qc'ed output matrix for ROSMAP round 2? I only found round 1 matrix but under round 2 folder, there is no matrix.
Appreciate your help!
Jenny Hi Jenny,
I believe the traits data for Round 1 is in a separate project here: https://www.synapse.org/Synapse:syn25006611/files/. But all the info in the traits files should also match up to the official metadata files for ROSMAP.
For AMP-AD Diverse Cohorts, I think the Emory team's traits data is using the old tissue categories. The consortium spent a long time harmonizing the metadata values for that study, so the values in the Diverse Cohorts metadata files should supersede those in the proteomics traits file! For tissue types, we confirmed with the various contributing groups that the regions are DLPFC and superior temporal gyrus. I'll talk to the Emory team about updating their traits files to match the harmonized metadata.
Thanks!
Abby Hello Abby,
Thank you for clarifying. Is there Round 1 trait data available like syn32835854? I am not sure if I need those for further analysis.
I also have a question regarding AMP-AD Diverse cohort proteomics data. After I merged three metadata syn51753257, I found the tissues were from DLPFC and superior temporal gyrus, however in syn55249983 and syn55249984, the samples were from TCX and frontal. Are they corresponding to each other?
Jenny Hi Jenny,
To get the sample and phenotype traits for the ROSMAP proteomics data, you can join the following metadata files:
* TMT assay metadata syn21323404 - maps specimenIDs to TMT batch and channel
* biospecimen metadata syn21323366 - maps specimenIDs to individualIDs
* clinical metadata syn3191087 - maps individualIDs to phenotype data and ROSMAP projids
That should give you the full set of metadata we have available for the Round 1 TMT proteomics data. Let me know if you run into any issues!
Abby