GSE62944_Tumor_TPM
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 (10; min: 8)
Results: PASS
First 5 columns and 5 rows of data.tsv.gz:
| Sample | 1/2-SBSRNA4 | A1BG | A1BG-AS1 | A1CF |
|---|---|---|---|---|
| TCGA-02-0047-01A-01R-1849-01 | 2.34180779897709 | 11.7173931223676 | 1.33274150888264 | 0.00783961263378836 |
| TCGA-02-0055-01A-01R-1849-01 | 1.64575215578575 | 24.7763572132346 | 1.08603706301478 | 0.015495311808889 |
| TCGA-02-2483-01A-01R-1849-01 | 2.43263380829254 | 20.2648719245462 | 1.09297209133143 | 0.00479039331850954 |
| TCGA-02-2485-01A-01R-1849-01 | 2.04036406475485 | 5.1177123833555 | 0.707189363771972 | 0.00585469442145148 |
Columns: 23369 Rows: 9265
“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 |
|---|---|---|
| TCGA-02-0047-01A-01R-1849-01 | Cancer_Type | Glioblastoma multiforme |
| TCGA-02-0047-01A-01R-1849-01 | form_completion_date | 2008-12-16 |
| TCGA-02-0047-01A-01R-1849-01 | gender | MALE |
| TCGA-02-0047-01A-01R-1849-01 | race | WHITE |
Columns: 3 Rows: 584808
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "informed_consent_verified" for all samples is the same ("YES"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "disease_code" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "project_code" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "eml4_alk_translocation_variant" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_er_positivity_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_pr_positivity_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_pr_positivity_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_positivity_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_positivity_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_signal_number" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_cent_17_signal_number" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "her2_cent17_counted_cells_count" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_cent17_her2_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_fish_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "number_of_lymphnodes_positive_by_ihc" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "cause_of_death_other" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "scca_tumor_marker" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "days_to_laboratory_procedure_tumor_marker_squamous" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "pathologic_stage" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "cells_used_for_analysis_source" for all samples is the same ("Bone marrow aspirate"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "initial_pathologic_dx_days_to" for all samples is the same ("0"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "history_chemical_exposure_other" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "diff_count_not_present_reason" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "type_of_analysis_other" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "site_of_primary_tumor_other" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "tumor_tissue_site_other" for all samples is the same ("[Not Applicable]|[Not Applicable]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "history_immunosuppresive_dx_other" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "other_metastatic_involvement_anatomic_site" for all samples is the same ("Lymph node"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "chemo_concurrent_reason_not_other" for all samples is the same ("Concurent chemo RT Ongoing-treatment delayed due t"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "radiation_type_other" for all samples is the same ("Whole pelvis split field"). 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
✅ Row 9: Success
✅ Row 10: Success
Results: PASS
Comparing samples in both files . . .
✅ Samples are the same in both “data.tsv.gz” & “metadata.tsv.gz”