BiomarkerBenchmark_GSE2109_Breast
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 |
|---|---|---|---|---|
| GSM38051 | 1.71086974882353 | -0.21158406125 | 2.18163119444444 | 0.8675377734375 |
| GSM38062 | 1.59672362352941 | -0.16073530875 | 2.24814632333333 | 1.061795885 |
| GSM38063 | 0.811448687647059 | -0.10039336625 | 2.11823704111111 | 0.9109764609375 |
| GSM38080 | 1.39695341294118 | -0.28130985125 | 2.40606065111111 | 0.488235835625 |
Columns: 20025 Rows: 261
“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 |
|---|---|---|
| GSM38051 | Alcohol_Consumption | Yes |
| GSM38051 | Days_from_Patient_Diagnosis_to_Excision | 8 |
| GSM38051 | Ethnic_Background | Caucasian |
| GSM38051 | Family_History_of_Cancer | No |
Columns: 3 Rows: 5881
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "Clinical_M" for all samples is the same ("0"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Clinical_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 "Pathological_Metastatic_Sites" for all samples is the same ("Pulmonary"). 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”