BiomarkerBenchmark_GSE2109_Kidney
Status: Complete
Testing Directory . . .
Results: PASS
Testing Configuration File . . .
✅ config.yaml contains all necessary configurations.
✅ Title is less than 100 characters
✅ description.md contains a description.
Results: PASS
Running Install . . .
Executing install.sh: Success
Results: PASS
Testing file paths:
✅ test_data.tsv exists.
✅ test_metadata.tsv exists.
✅ download.sh exists.
✅ install.sh exists.
✅ parse.sh exists.
✅ cleanup.sh exists.
✅ description.md exists.
✅ config.yaml exists.
Running user code . . .
Executing download.sh: Success
Executing parse.sh: Success
✅ data.tsv.gz was created and zipped correctly.
✅ metadata.tsv.gz was created and zipped correctly.
Results: PASS
Testing Key Files:
✅ test_data.tsv contains enough unique samples to test
✅ test_data.tsv contains enough test cases (8; min: 8)
✅ test_metadata.tsv contains enough unique samples to test
✅ test_metadata.tsv contains enough test cases (8; min: 8)
Results: PASS
First 5 columns and 5 rows of data.tsv.gz:
| Sample | ENSG00000000003 | ENSG00000000005 | ENSG00000000419 | ENSG00000000457 |
|---|---|---|---|---|
| GSM46825 | 1.56976304411765 | -0.04667038875 | 2.10052035 | 0.4140482690625 |
| GSM46826 | 1.67171784294118 | -0.01953416375 | 1.89430100444444 | 0.2049952940625 |
| GSM46847 | 1.672937 | -0.27605256375 | 1.91097481 | 0.2990809496875 |
| GSM46858 | 1.15044336235294 | -0.218941465 | 2.05204581888889 | 0.451392254375 |
Columns: 20025 Rows: 210
“data.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
Results: PASS
First 3 columns and 5 rows of metadata.tsv.gz:
| Sample | Variable | Value |
|---|---|---|
| GSM46825 | Alcohol_Consumption | No |
| GSM46825 | Clinical_Grade | 2 |
| GSM46825 | Clinical_M | 0 |
| GSM46825 | Clinical_N | 0 |
Columns: 3 Rows: 3344
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "Pathological_Stage_During_or_Following_Multimodality_Therapy" for all samples is the same ("No"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Primary_Site" for all samples is the same ("Kidney"). This variable has been removed from metadata.tsv.gz
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
Results: PASS
Comparing samples in both files . . .
✅ Samples are the same in both “data.tsv.gz” & “metadata.tsv.gz”