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Release 2023-05-17-1317
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@TDCasasent
TDCasasent committed May 22, 2023
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1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/BoxPlot/AllSample-Data/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/BoxPlot/AllSample-RLE/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/BoxPlot/Group-Mean/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/CDP/error.log
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Clustering not possible
4 changes: 4 additions & 0 deletions testing_static/BEVIndex/errors/DSCOverview.tsv
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dataset Overall-DSC Overall-DSC-pvalue DSC(1,2) DSC-pvalue(1,2) DSC(1,3) DSC-pvalue(1,3) DSC(1,4) DSC-pvalue(1,4) DSC(2,3) DSC-pvalue(2,3) DSC(2,4) DSC-pvalue(2,4) DSC(3,4) DSC-pvalue(3,4)
/PCA/BatchId/ManyToMany 0.178777527027741 <0.0005 0.166400440202471 <0.0005 0.1611961070068 <0.0005 0.160960175649534 <0.0005 0.237152915888221 <0.0005 0.248690401637216 <0.0005 0.226817208923315 <0.0005
/PCA/ShipDate/ManyToMany 0.14838949950449 <0.0005 0.142646809555771 <0.0005 0.135012267113029 <0.0005 0.139438011189922 <0.0005 0.182307569880918 <0.0005 0.219598331440616 <0.0005 0.172552400227154 <0.0005
/PCA/TSS/ManyToMany 0.138723719311791 <0.0005 0.132800486456796 <0.0005 0.126225986871273 <0.0005 0.1288490961162 <0.0005 0.172264733581014 <0.0005 0.192683792584538 <0.0005 0.156412315939838 <0.0005
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/Discrete/BatchId/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/Discrete/ShipDate/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/Discrete/TSS/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/HierarchicalClustering/error.log
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HC not calculated -- too many nulls, NAs, infinities, or no deviation
4 changes: 4 additions & 0 deletions testing_static/BEVIndex/errors/NGCHM/error.log
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No UMAP -Error in if (neighbors > (dim(pca_data$x)[0])) {: argument is of length zero
- 2022_05_23_0838/GDC/current/TCGA
TCGA-KIRC/Gene/Level/Copy/Number/ASCAT2
Original-Analyzed/continuous/noXY
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/PCA/BatchId/ManyToMany/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/PCA/ShipDate/ManyToMany/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/PCA/TSS/ManyToMany/error.log
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Clustering not possible
1 change: 1 addition & 0 deletions testing_static/BEVIndex/errors/SupervisedClustering/Batches/error.log
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Clustering not possible
4 changes: 4 additions & 0 deletions testing_static/BEVIndex/errors/UMAP/error.log
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No UMAP -Error in if (neighbors > (dim(pca_data$x)[0])) {: argument is of length zero
- 2022_05_23_0838/GDC/current/TCGA
TCGA-KIRC/Gene/Level/Copy/Number/ASCAT2
Original-Analyzed/continuous/noXY
174 changes: 174 additions & 0 deletions testing_static/BEVIndex/errors/json.txt
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{
"SourceID": "SOURCE_ID",
"source": "unknown - user data",
"variant": "unknown - user data",
"project": "unknown - user data",
"subProject": "unknown - user data",
"category": "unknown - user data",
"platform": "unknown - user data",
"data": "unknown - user data",
"algorithm": "unknown - user data",
"details": "unknown - user data",
"version": "unknown - user data",
"mbatch": {
"MBatchID": "MBATCH_ID",
"mbatch_run": "VERSION_STAMP",
"dataset_type": "VERSION_TYPE",
"matrix": "",
"batchdata": "",
"dropdown_label": "Algorithm",
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"box_data": "/BoxPlot/AllSample-Data/BoxPlot_AllSample-Data_BoxData-NA.tsv",
"box_histogram": "/BoxPlot/AllSample-Data/BoxPlot_AllSample-Data_Histogram-NA.tsv"
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},
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{
"entry_label": "Dispersion Separability Criterion",
"diagram_type": "DSC",
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{
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"legend_image": "/HierarchicalClustering/HierarchicalClustering_Legend-ALL.png",
"hc_data": "/HierarchicalClustering/HCData.tsv",
"hc_order": "/HierarchicalClustering/HCOrder.tsv"
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"entry_label": "Kruskal-Wallis / Dunn\u0027s Test",
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"diagram_image": "/Discrete/BatchId/KW_Dunns_Diagram.PNG",
"kwd_kwddata": "/Discrete/BatchId/KW_Dunns_Diagram.tsv"
},
{
"entry_label": "ShipDate",
"diagram_type": "discrete",
"diagram_image": "/Discrete/ShipDate/KW_Dunns_Diagram.PNG",
"kwd_kwddata": "/Discrete/ShipDate/KW_Dunns_Diagram.tsv"
},
{
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"diagram_image": "/Discrete/TSS/KW_Dunns_Diagram.PNG",
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"ngchm": "/NGCHM/error_ngchm.ngchm.html"
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},
{
"entry_label": "PCA+",
"dropdown_label": "Batch Type",
"dropdown_entries": [
{
"entry_label": "BatchId",
"diagram_type": "pca",
"pca_annotations": "/PCA/BatchId/ManyToMany/PCAAnnotations.tsv",
"pca_values": "/PCA/BatchId/ManyToMany/PCAValues.tsv"
},
{
"entry_label": "ShipDate",
"diagram_type": "pca",
"pca_annotations": "/PCA/ShipDate/ManyToMany/PCAAnnotations.tsv",
"pca_values": "/PCA/ShipDate/ManyToMany/PCAValues.tsv"
},
{
"entry_label": "TSS",
"diagram_type": "pca",
"pca_annotations": "/PCA/TSS/ManyToMany/PCAAnnotations.tsv",
"pca_values": "/PCA/TSS/ManyToMany/PCAValues.tsv"
}
]
},
{
"entry_label": "Supervised Clustering",
"dropdown_label": "Batch Type",
"dropdown_entries": [
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"diagram_type": "ngchm",
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"legend_image": "/SupervisedClustering/Batches/SupervisedClust_Legend-Error.png",
"ngchm": "/SupervisedClustering/Batches/Error_ngchm.ngchm.html"
}
]
},
{
"entry_label": "UMAP",
"dropdown_label": "Batch Type",
"dropdown_entries": [
{
"entry_label": "error.log",
"diagram_type": "umap",
"umap_batches": "/UMAP/error.log/UMAP_Data-batc.tsv",
"umap_umapdat": "/UMAP/error.log/UMAP_Data-umap.tsv"
}
]
}
]
},
"notice": ""
}
30 changes: 30 additions & 0 deletions testing_static/COMPARE/AN003501_UMAP_Data-batc.tsv
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Samples Batches
1aCre wildtype
1bCre wildtype
1cCre wildtype
2aCre wildtype
2bCre wildtype
2cCre wildtype
3aDNT mutant
3bDNT mutant
3cCre wildtype
4aDNT mutant
4bDNT mutant
4cDNT mutant
5cDNT mutant
6cDNT mutant
B cells_DNT_GPL analysis 1-S01_DNT mutant
B cells_DNT_GPL analysis 1-S02_Cre wildtype
B cells_DNT_GPL analysis 1-S03_DNT mutant
B cells_DNT_GPL analysis 1-S04_Cre wildtype
B cells_DNT_GPL analysis 1-S05_DNT mutant
B cells_DNT_GPL analysis 1-S06_Cre wildtype
B cells_DNT_GPL analysis 2b-S01_Cre1 wildtype
B cells_DNT_GPL analysis 2b-S02_DNT2 mutant
B cells_DNT_GPL analysis 2b-S03_Cre3 wildtype
B cells_DNT_GPL analysis 2b-S04_DNT4 mutant
B cells_DNT_GPL analysis 2b-S05_Cre5 wildtype
B cells_DNT_GPL analysis 2b-S06_DNT6 mutant
B cells_DNT_GPL analysis 2b-S07_Cre7 wildtype
B cells_DNT_GPL analysis 2b-S08_DNT8 mutant
B cells_DNT_GPL analysis 2b-S10_DNT10 mutant
98 changes: 49 additions & 49 deletions testing_static/COMPARE/HierarchicalClustering_Structures.tsv
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16 changes: 16 additions & 0 deletions testing_static/COMPARE/MANOVA_Structures.tsv
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key value
title Test
method Shapiro-Wilk normality test
pvalue <0.0005
Residuals 0.73286596746068
Type 0.127490358799937
BatchId 0.0331990448442522
TSS 0.0295698212473222
Type:BatchId 0.0107323188041473
Type:TSS 0.00643794589567752
BatchId:TSS 0.0551796537159235
Type:BatchId:TSS 0.00452488923206235
labels Residuals (73.3%)==|==Type (14.9%)==|==BatchId (10.4%)==|==TSS (9.6%)
version MBatch Version: BEA_VERSION_TIMESTAMP
colornames Residuals==|==Type==|==BatchId==|==TSS==|==Type:BatchId==|==Type:TSS==|==BatchId:TSS==|==Type:BatchId:TSS
colors #80FF00,#8000FF,#FF0000,#00FFFF,NA,NA,NA,NA
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