Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	BRCAcors.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	stdout.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	BRCAqa.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	gp_execution_log.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	nozzle.html	report	Level_3	html	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
rsseg	all_data_by_genes.txt	gdac.broadinstitute.org_BRCA.CopyNumber_Gistic2.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	nozzle.RData	report	Level_3	RData	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	BRCAcors.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	stdout.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	BRCAqa.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	gp_execution_log.txt	Correlation_reslut	Level_3	txt	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	nozzle.html	report	Level_3	html	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
mExp	BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_BRCA.mRNAseq_Preprocess.Level_4.2012082500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10052:17	Correlate_CopyNumber_vs_mRNAseq_2012082500	nozzle.RData	report	Level_3	RData	gdac.broadinstitute.org_BRCA.Correlate_CopyNumber_vs_mRNAseq.Level_3.2012082500.0.0	yes
