BiomarkerBenchmark_GSE2109_Endometrium
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 |
|---|---|---|---|---|
| GSM38067 | 2.51174563411765 | -0.06398938 | 2.41418058111111 | 0.532588206875 |
| GSM38084 | 2.04430493 | -0.17738299125 | 2.25459530444444 | 0.2675048278125 |
| GSM46867 | 2.35919298411765 | -0.10473930125 | 2.42252435777778 | 0.5238796334375 |
| GSM46912 | 2.55878040764706 | -0.2314555575 | 2.05281890111111 | 0.48969787375 |
Columns: 20025 Rows: 52
“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 |
|---|---|---|
| GSM38067 | Alcohol_Consumption | Yes |
| GSM38067 | Days_from_Patient_Diagnosis_to_Excision | 42 |
| GSM38067 | Ethnic_Background | Caucasian |
| GSM38067 | Family_History_of_Cancer | No |
Columns: 3 Rows: 661
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "Histology" for all samples is the same ("Endometrioid carcinoma"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Primary_Site" for all samples is the same ("Endometrium"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Pathological_Multiple_Tumors" for all samples is the same ("No"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Ethnic_Background" for all samples is the same ("Caucasian"). 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”