Broad GDAC stddata__2013_07_15 Run Status : LUSC

Tumor	BCR	Clinical	CN	LowP	Methylation	mRNA	mRNAseq	miR	miRseq	RPPA	MAF
LUSC	494	388	416	0	493	154	375	0	468	195	178

Note that the links below require Broad internal Firehose login credentials.

	Pipeline Dataset	Not Available	Successful
1	Clinical_Pick_Tier1	0	1
2	CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB	1	0
3	CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT	1	0
4	CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB	1	0
5	CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT	1	0
6	CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB	1	0
7	CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT	1	0
8	CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB	1	0
9	CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT	1	0
10	CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB	1	0
11	CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT	1	0
12	Merge_Clinical	0	1
13	Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_2__bioassay_data_transformation__data	1	0
14	Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg	0	1
15	Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_2__lowess_global_normalization__data	1	0
16	Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg	1	0
17	Merge_cna__hg_cgh_244a__mskcc_org__Level_2__bioassay_data_transformation__data	1	0
18	Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg	1	0
19	Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_2__lowess_global_normalization__data	1	0
20	Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg	0	1
21	Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg	1	0
22	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data	0	1
23	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data	0	1
24	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data	0	1
25	Merge_methylation__humanmethylation27__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data	1	0
26	Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data	0	1
27	Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data	0	1
28	Merge_methylation__illuminadnamethylation_oma003_cpi__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data	1	0
29	Merge_mirna__h_mirna_8x15k__unc_edu__Level_2__unc_quantile_normalization__data	1	0
30	Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data	1	0
31	Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_2__unc_quantile_normalization__data	1	0
32	Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data	1	0
33	Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data	0	1
34	Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data	0	1
35	Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data	0	1
36	Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data	0	1
37	Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data	0	1
38	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data	1	0
39	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data	1	0
40	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data	1	0
41	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data	1	0
42	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data	1	0
43	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data	1	0
44	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data	1	0
45	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data	1	0
46	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data	1	0
47	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data	0	1
48	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data	0	1
49	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data	0	1
50	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data	1	0
51	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data	1	0
52	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data	1	0
53	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data	1	0
54	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data	1	0
55	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data	0	1
56	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data	0	1
57	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data	0	1
58	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data	0	1
59	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data	0	1
60	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__after_5NN_copy_number__data	1	0
61	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed	0	1
62	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copynumber_byallele__data	1	0
63	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copy_number__data	1	0
64	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data	1	0
65	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__no_outlier_copy_number__data	1	0
66	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg	0	1
67	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg	0	1
68	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg	0	1
69	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg	0	1
70	Merge_snp__human1mduo__hudsonalpha_org__Level_1__XandYintensity__data	1	0
71	Merge_snp__human1mduo__hudsonalpha_org__Level_2__B_allele_freq__data	1	0
72	Merge_snp__human1mduo__hudsonalpha_org__Level_2__Delta_B_allele_freq__data	1	0
73	Merge_snp__human1mduo__hudsonalpha_org__Level_2__genotyping__data	1	0
74	Merge_snp__human1mduo__hudsonalpha_org__Level_2__Normal_LogR__data	1	0
75	Merge_snp__human1mduo__hudsonalpha_org__Level_2__Paired_LogR__data	1	0
76	Merge_snp__human1mduo__hudsonalpha_org__Level_2__Unpaired_LogR__data	1	0
77	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg	0	1
78	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg	0	1
79	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg	0	1
80	Merge_snp__humanhap550__hudsonalpha_org__Level_1__XandYintensity__data	1	0
81	Merge_snp__humanhap550__hudsonalpha_org__Level_2__B_allele_freq__data	1	0
82	Merge_snp__humanhap550__hudsonalpha_org__Level_2__Delta_B_allele_freq__data	1	0
83	Merge_snp__humanhap550__hudsonalpha_org__Level_2__genotyping__data	1	0
84	Merge_snp__humanhap550__hudsonalpha_org__Level_2__Normal_LogR__data	1	0
85	Merge_snp__humanhap550__hudsonalpha_org__Level_2__Paired_LogR__data	1	0
86	Merge_snp__humanhap550__hudsonalpha_org__Level_2__Unpaired_LogR__data	1	0
87	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg	1	0
88	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg	1	0
89	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg	1	0
90	Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	1	0
91	Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	1	0
92	Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	1	0
93	Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	1	0
94	Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	0	1
95	Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	0	1
96	Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data	0	1
97	Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data	0	1
98	mRNAseq_Preprocess	0	1
99	Mutation_Packager_Calls	0	1
100	Mutation_Packager_Coverage	0	1
101	RPPA_AnnotateWithGene	0	1
	Total	63	38

This table generated on Fri Jul 19 16:59:06 2013

Broad GDAC Standard Data Status stddata__2013_07_15 Run for Tumor Type: LUSC

Broad GDAC Standard Data Status
stddata__2013_07_15 Run for Tumor Type: LUSC