BiomarkerBenchmark_GSE2109_Colon
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 |
|---|---|---|---|---|
| GSM38055 | 2.88366766705882 | 0.55310198125 | 2.28798520777778 | 0.5766371840625 |
| GSM38061 | 1.57436517764706 | 1.59950003125 | 2.26277430666667 | 0.621868049375 |
| GSM38074 | 2.58037697294118 | -0.00589102874999999 | 2.63275796333333 | 0.45848329875 |
| GSM38075 | 2.13742352764706 | -0.14214627625 | 2.68426196333333 | 0.477348534375 |
Columns: 20025 Rows: 248
“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 |
|---|---|---|
| GSM38055 | Alcohol_Consumption | Yes |
| GSM38055 | Days_from_Patient_Diagnosis_to_Excision | 13 |
| GSM38055 | Diagnosis_made_by | Colonoscopy |
| GSM38055 | Ethnic_Background | Caucasian |
Columns: 3 Rows: 4770
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "Clinical_Stage" for all samples is the same ("1"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Clinical_Dukes_Stage" for all samples is the same ("A"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Clinical_T" for all samples is the same ("2"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Clinical_N" for all samples is the same ("0"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Clinical_Grade" for all samples is the same ("2"). 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”