Hello.

I am working with the LINCS dataset and I have access to the Level 3 and Level 4 data. I want to convert the Level 3 data to Level 4 using the method provided in the documentation. "Level 4 - ZS - Z-scores for each gene based on Level 3 with respect to the entire plate population". This line can be found in https://clue.io/connectopedia/data_levels.

However, using the method of z-score normalization, I am unable to replicate the scores of Level 4. I read in another place to try Robust Z-Scores and Modified Z-scores which involve the use of median. But I was still unable to find the solution.

Has anyone tried this replication from Level 3 to Level 4. Would appreciate the guidance.

Thank you.

PS: Another description can be found here: https://rdrr.io/github/yduan004/signatureSearch_data/man/lincs.html It states that after level 3: A robust z-scoring procedure was used to generate differential expression values from the normalized profiles which results in Level 4.