Broad GDAC Standard Data Status
stddata__2013_02_22 Run for Tumor Type: OV
Tumor
BCR
Clinical
CN
LowP
Methylation
mRNA
mRNAseq
miR
miRseq
RPPA
MAF
OV
592
580
566
0
584
574
297
570
454
412
316
Note that the links below require Broad internal Firehose login credentials.
Pipeline Dataset
Not Available
Available
InProcess
Successful
Unsuccessful
1
Clinical_Pick_Tier1
0
0
0
1
0
2
CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB
1
0
0
0
0
3
CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT
1
0
0
0
0
4
CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB
1
0
0
0
0
5
CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT
1
0
0
0
0
6
CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB
1
0
0
0
0
7
CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT
1
0
0
0
0
8
CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB
1
0
0
0
0
9
CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT
1
0
0
0
0
10
CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB
1
0
0
0
0
11
CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT
1
0
0
0
0
12
Merge_Clinical
0
0
0
1
0
13
Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_2__bioassay_data_transformation__data
1
0
0
0
0
14
Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg
0
0
0
1
0
15
Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_2__lowess_global_normalization__data
1
0
0
0
0
16
Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg
0
0
0
1
0
17
Merge_cna__hg_cgh_244a__mskcc_org__Level_2__bioassay_data_transformation__data
1
0
0
0
0
18
Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
1
0
0
0
0
19
Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_2__lowess_global_normalization__data
1
0
0
0
0
20
Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg
0
0
0
1
0
21
Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
1
0
0
0
0
22
Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data
0
0
0
1
0
23
Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
0
0
0
1
0
24
Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data
0
0
0
1
0
25
Merge_methylation__humanmethylation27__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
0
0
0
0
26
Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
0
0
0
1
0
27
Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
1
0
0
0
0
28
Merge_methylation__illuminadnamethylation_oma003_cpi__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
0
0
0
0
29
Merge_mirna__h_mirna_8x15k__unc_edu__Level_2__unc_quantile_normalization__data
1
0
0
0
0
30
Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
1
0
0
0
0
31
Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_2__unc_quantile_normalization__data
1
0
0
0
0
32
Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
0
0
0
1
0
33
Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
1
0
0
0
0
34
Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
1
0
0
0
0
35
Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
0
0
0
1
0
36
Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
0
0
0
1
0
37
Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
0
0
0
1
0
38
Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data
1
0
0
0
0
39
Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data
1
0
0
0
0
40
Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
1
0
0
0
0
41
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
1
0
0
0
0
42
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data
1
0
0
0
0
43
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data
1
0
0
0
0
44
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data
0
0
0
1
0
45
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data
0
0
0
1
0
46
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
0
0
0
1
0
47
Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
1
0
0
0
0
48
Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
1
0
0
0
0
49
Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data
1
0
0
0
0
50
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data
0
0
0
1
0
51
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data
0
0
0
1
0
52
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
0
0
0
1
0
53
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
0
0
0
1
0
54
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data
0
0
0
1
0
55
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__after_5NN_copy_number__data
1
0
0
0
0
56
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed
0
0
0
1
0
57
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copynumber_byallele__data
1
0
0
0
0
58
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copy_number__data
1
0
0
0
0
59
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data
1
0
0
0
0
60
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__no_outlier_copy_number__data
1
0
0
0
0
61
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg
0
0
0
1
0
62
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
0
0
0
1
0
63
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
0
0
0
1
0
64
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg
0
0
0
1
0
65
Merge_snp__human1mduo__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
66
Merge_snp__human1mduo__hudsonalpha_org__Level_2__B_allele_freq__data
1
0
0
0
0
67
Merge_snp__human1mduo__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
1
0
0
0
0
68
Merge_snp__human1mduo__hudsonalpha_org__Level_2__genotyping__data
1
0
0
0
0
69
Merge_snp__human1mduo__hudsonalpha_org__Level_2__Normal_LogR__data
1
0
0
0
0
70
Merge_snp__human1mduo__hudsonalpha_org__Level_2__Paired_LogR__data
1
0
0
0
0
71
Merge_snp__human1mduo__hudsonalpha_org__Level_2__Unpaired_LogR__data
1
0
0
0
0
72
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg
0
0
0
1
0
73
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg
0
0
0
1
0
74
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg
0
0
0
1
0
75
Merge_snp__humanhap550__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
76
Merge_snp__humanhap550__hudsonalpha_org__Level_2__B_allele_freq__data
1
0
0
0
0
77
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
1
0
0
0
0
78
Merge_snp__humanhap550__hudsonalpha_org__Level_2__genotyping__data
1
0
0
0
0
79
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Normal_LogR__data
1
0
0
0
0
80
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Paired_LogR__data
1
0
0
0
0
81
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Unpaired_LogR__data
1
0
0
0
0
82
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg
1
0
0
0
0
83
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg
1
0
0
0
0
84
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
85
Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
86
Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
87
Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
0
0
0
1
0
88
Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
0
0
0
1
0
89
Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
0
0
0
1
0
90
Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
0
0
0
1
0
91
Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data
0
0
0
1
0
92
Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data
0
0
0
1
0
93
mRNAseq_Preprocess
0
0
0
1
0
94
Mutation_Packager_Calls
0
0
0
1
0
95
Mutation_Packager_Coverage
0
0
0
1
0
96
RPPA_AnnotateWithGene
0
0
0
1
0
97
TR-Clinical_Pick_Tier1
1
0
0
0
0
98
TR-CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB
1
0
0
0
0
99
TR-CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT
1
0
0
0
0
100
TR-CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB
1
0
0
0
0
101
TR-CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT
1
0
0
0
0
102
TR-CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB
1
0
0
0
0
103
TR-CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT
1
0
0
0
0
104
TR-CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB
1
0
0
0
0
105
TR-CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT
1
0
0
0
0
106
TR-CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB
1
0
0
0
0
107
TR-CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT
1
0
0
0
0
108
TR-Merge_Clinical
1
0
0
0
0
109
TR-Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_2__bioassay_data_transformation__data
1
0
0
0
0
110
TR-Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg
0
0
0
1
0
111
TR-Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_2__lowess_global_normalization__data
1
0
0
0
0
112
TR-Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg
1
0
0
0
0
113
TR-Merge_cna__hg_cgh_244a__mskcc_org__Level_2__bioassay_data_transformation__data
1
0
0
0
0
114
TR-Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
1
0
0
0
0
115
TR-Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_2__lowess_global_normalization__data
1
0
0
0
0
116
TR-Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg
0
0
0
1
0
117
TR-Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
1
0
0
0
0
118
TR-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data
0
0
0
1
0
119
TR-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
0
0
0
1
0
120
TR-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data
0
0
0
1
0
121
TR-Merge_methylation__humanmethylation27__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
0
0
0
0
122
TR-Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
0
0
0
1
0
123
TR-Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
1
0
0
0
0
124
TR-Merge_methylation__illuminadnamethylation_oma003_cpi__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
0
0
0
0
125
TR-Merge_mirna__h_mirna_8x15k__unc_edu__Level_2__unc_quantile_normalization__data
1
0
0
0
0
126
TR-Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
1
0
0
0
0
127
TR-Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_2__unc_quantile_normalization__data
1
0
0
0
0
128
TR-Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
0
0
0
1
0
129
TR-Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
1
0
0
0
0
130
TR-Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
1
0
0
0
0
131
TR-Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
0
0
0
1
0
132
TR-Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
0
0
0
1
0
133
TR-Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
1
0
0
0
0
134
TR-Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data
1
0
0
0
0
135
TR-Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data
1
0
0
0
0
136
TR-Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
1
0
0
0
0
137
TR-Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
1
0
0
0
0
138
TR-Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data
1
0
0
0
0
139
TR-Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data
1
0
0
0
0
140
TR-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data
0
0
0
1
0
141
TR-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data
0
0
0
1
0
142
TR-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
0
0
0
1
0
143
TR-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
1
0
0
0
0
144
TR-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
1
0
0
0
0
145
TR-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data
1
0
0
0
0
146
TR-Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data
0
0
0
1
0
147
TR-Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data
0
0
0
1
0
148
TR-Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
0
0
0
1
0
149
TR-Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
0
0
0
1
0
150
TR-Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data
0
0
0
1
0
151
TR-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__after_5NN_copy_number__data
1
0
0
0
0
152
TR-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed
0
0
0
1
0
153
TR-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copynumber_byallele__data
1
0
0
0
0
154
TR-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copy_number__data
1
0
0
0
0
155
TR-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data
1
0
0
0
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1
0
0
0
0
468
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
469
NB-Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
470
NB-Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
471
NB-Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
472
NB-Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
473
NB-Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
474
NB-Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
475
NB-Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data
1
0
0
0
0
476
NB-Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data
1
0
0
0
0
477
NB-mRNAseq_Preprocess
1
0
0
0
0
478
NB-Mutation_Packager_Calls
1
0
0
0
0
479
NB-Mutation_Packager_Coverage
1
0
0
0
0
480
NB-RPPA_AnnotateWithGene
1
0
0
0
0
Total
342
0
0
138
0
This table generated on Mon Mar 4 14:12:20 2013