BiomarkerBenchmark_GSE43176
Status: Complete
Testing Directory . . .
Results: PASS
Testing Configuration File . . .
✅ config.yaml contains all necessary configurations.
✅ Title is less than 300 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 |
|---|---|---|---|---|
| GSM1057836 | -0.04165015 | -0.11731505125 | 0.74634068 | -0.10284184173913 |
| GSM1057837 | -0.102259795882353 | -0.2626097925 | 1.11522876333333 | -0.0383493347826087 |
| GSM1057838 | -0.222879033529412 | -0.3286507475 | 1.06145151111111 | -0.0790448365217391 |
| GSM1057839 | -0.0998797111764706 | -0.22587852 | 1.21281470444444 | 0.06549571 |
Columns: 11833 Rows: 104
“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 |
|---|---|---|
| GSM1057836 | cytogenetics | 45,X,-Y,t(8;21)(q22;q22),del(10)(p14) |
| GSM1057836 | disease_state | AML |
| GSM1057836 | fab | M4E |
| GSM1057836 | nras_status | NRAS wild type |
Columns: 3 Rows: 514
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "disease_state" for all samples is the same ("AML"). 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”