MPNST datasets' "improve_sample_id" not aligning with the coderdata version 0.1.26

[moonchangin]

Issue: Misaligned improve_sample_id in MPNST Databases

Files:

• mpnst_experiments.tsv
• mpnst_transcriptomics.csv.gz

Description:

There appears to be a misalignment between the improve_sample_id fields in two MPNST database files. This discrepancy wasn't present in the initial MPNST data version I created, but has been noticeable recently (data is from version 0.1.26).

Details:

• Gene Expression File unique Sample IDs (mpnst_gene_exp['improve_sample_id']):

  {5124, 5125, 5126, 5127, 5128, 5129, 5132, 5133, 5134, 5135, 5136, 5137, 5138, 5139, 5140, 5141, 5142, 5143, 5154, 5155, 5156, 5157, 5158, 5159, 5162, 5163, 5164, 5165, 5166, 5167, 5168, 5169, 5170, 5171, 5172}

• Experiments File unique Sample IDs (mpnst_experiments['improve_sample_id']):

  {5152, 5153, 5144, 5145, 5146, 5147, 5148, 5149, 5150, 5151}

Expected Behavior:

Both files should have aligned improve_sample_id values for consistent data analysis and integrity.

Actual Behavior:

The improve_sample_id sets from the transcriptomic and experiment files do not match, indicating potential issues in data alignment or entry.

Steps to Reproduce:

1. Load the data from both files.
2. Extract and compare the unique improve_sample_id sets as shown above.
3. Observe the discrepancy between the two sets.

Additional Context:

This alignment issue may affect data analysis and integrity, requiring a thorough investigation and correction of the sample IDs in the relevant databases.

[sgosline]

Jeremy can you please confirm that no other sample files have issues, then rebuild the MPNST data per the build_locally script? You shoudn't have to rebuilt everything.

[jjacobson95]

Looking like there may be some other issues with hcmi and broad_sanger samples files. I'll create separate issues with more information