Which set of GSEA data is equivalent to modzs.gctx

[krishbharat96]

Hello Daniel,

I am in the process of creating auto-update scripts for all the nodes with hetio, and in order to do that, I will need a copy of the most up-to-date modzs.gctx file. I know that GSEA has some LINCS datasets in there, and I was curious which files best correspond to the modzs file that you used in this repository. Any input or feedback would be greatly appreciated. Thank you!

Best,
Krish

[dhimmel]

which files best correspond to the modzs file that you used in this repository

I think this issue is similar to #3. The modzs.gctx file used for this analysis is available on figshare. I would suggest following the README instruction:

To recreate this analysis rather than just use the results, users should retrieve modzs.gctx from figshare and place it in the download directory.

While the LINCS L1000 team no longer distributes this file at lincscloud, I believe it does contain the most recent differential expression data available, which is now distributed via GEO.

See the comment at #4 (comment):

Yes, the old modzs.gctx file you obtained from lincslcoud was indeed generated using the population-based z-scoring procedure, aka ZSPC.

It is possible that clue.io has an updated modzs file, although I don't think this resource is openly licensed.

[krishbharat96]

Thank you: this is very helpful. I really appreciate all your help!

Best,
Krish