Sometimes, not regularly, some analysis are missing reactome_links like the following
35c9c72e-6848-11ee-9987-4681c6c0c82f, even though it was published with create_reactome_visualization parameter true:
This is quite problematic as it makes the analsysis results redirect to gsa home page :/
{
"methodName": "Camera",
"parameters": [
{
"name": "use_interactors",
"value": false
},
{
"name": "include_disease_pathways",
"value": true
},
{
"name": "max_missing_values",
"value": 0.5
},
{
"name": "create_reactome_visualization",
"value": true
},
{
"name": "create_reports",
"value": false
},
{
"name": "email",
"value": ""
},
{
"name": "reactome_server",
"value": "production"
},
{
"name": "discrete_norm_function",
"value": "TMM"
},
{
"name": "continuous_norm_function",
"value": "none"
}
],
"datasets": [
{
"data": "EXAMPLE_MEL_RNA",
"name": "Melanoma RNA-seq example",
"type": "rnaseq_counts",
"parameters": [
{
"name": "max_missing_values",
"value": 0.5
},
{
"name": "discrete_norm_function",
"value": "TMM"
},
{
"name": "continuous_norm_function",
"value": "none"
}
],
"design": {
"analysisGroup": [
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM",
"MOCK",
"MCM"
],
"samples": [
"X195.13",
"X195.14",
"X195.19",
"X195.20",
"X197.11",
"X197.12",
"X197.13",
"X197.14",
"X197.1",
"X197.2",
"X197.3",
"X197.4",
"X197.5",
"X197.6",
"X197.7",
"X197.8"
],
"comparison": {
"group1": "MOCK",
"group2": "MCM"
},
"patient.id": [
"P1",
"P1",
"P2",
"P2",
"P1",
"P1",
"P2",
"P2",
"P3",
"P3",
"P3",
"P3",
"P4",
"P4",
"P4",
"P4"
],
"cell.type": [
"TIBC",
"TIBC",
"PBMCB",
"PBMCB",
"PBMCB",
"PBMCB",
"TIBC",
"TIBC",
"TIBC",
"TIBC",
"PBMCB",
"PBMCB",
"TIBC",
"TIBC",
"PBMCB",
"PBMCB"
]
}
}
]
}
Sometimes, not regularly, some analysis are missing reactome_links like the following
35c9c72e-6848-11ee-9987-4681c6c0c82f, even though it was published with create_reactome_visualization parameter true:
This is quite problematic as it makes the analsysis results redirect to gsa home page :/
{ "methodName": "Camera", "parameters": [ { "name": "use_interactors", "value": false }, { "name": "include_disease_pathways", "value": true }, { "name": "max_missing_values", "value": 0.5 }, { "name": "create_reactome_visualization", "value": true }, { "name": "create_reports", "value": false }, { "name": "email", "value": "" }, { "name": "reactome_server", "value": "production" }, { "name": "discrete_norm_function", "value": "TMM" }, { "name": "continuous_norm_function", "value": "none" } ], "datasets": [ { "data": "EXAMPLE_MEL_RNA", "name": "Melanoma RNA-seq example", "type": "rnaseq_counts", "parameters": [ { "name": "max_missing_values", "value": 0.5 }, { "name": "discrete_norm_function", "value": "TMM" }, { "name": "continuous_norm_function", "value": "none" } ], "design": { "analysisGroup": [ "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM", "MOCK", "MCM" ], "samples": [ "X195.13", "X195.14", "X195.19", "X195.20", "X197.11", "X197.12", "X197.13", "X197.14", "X197.1", "X197.2", "X197.3", "X197.4", "X197.5", "X197.6", "X197.7", "X197.8" ], "comparison": { "group1": "MOCK", "group2": "MCM" }, "patient.id": [ "P1", "P1", "P2", "P2", "P1", "P1", "P2", "P2", "P3", "P3", "P3", "P3", "P4", "P4", "P4", "P4" ], "cell.type": [ "TIBC", "TIBC", "PBMCB", "PBMCB", "PBMCB", "PBMCB", "TIBC", "TIBC", "TIBC", "TIBC", "PBMCB", "PBMCB", "TIBC", "TIBC", "PBMCB", "PBMCB" ] } } ] }