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]
GDAC_RPPA_preprocess:Rppafile	LUSC.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt	gdac.broadinstitute.org_LUSC.Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.antibody_annotation.txt	RPPA-antibody_annotation	Level_3	txt	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes
GDAC_RPPA_preprocess:Rppafile	LUSC.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt	gdac.broadinstitute.org_LUSC.Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.rppa.txt	RPPA_Level3_mapped	Level_3	txt	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes
GDAC_RPPA_preprocess:Rppafile	LUSC.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt	gdac.broadinstitute.org_LUSC.Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.rppa.png	PNG	Level_3	png	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes
GDAC_RPPA_preprocess_annotations:annot_file	LUSC.2015_08_19__00_00_14.antibody_annotation.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.antibody_annotation.txt	RPPA-antibody_annotation	Level_3	txt	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes
GDAC_RPPA_preprocess_annotations:annot_file	LUSC.2015_08_19__00_00_14.antibody_annotation.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.rppa.txt	RPPA_Level3_mapped	Level_3	txt	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes
GDAC_RPPA_preprocess_annotations:annot_file	LUSC.2015_08_19__00_00_14.antibody_annotation.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:11104:3	RPPA_AnnotateWithGene_2016012800	LUSC.rppa.png	PNG	Level_3	png	gdac.broadinstitute.org_LUSC.RPPA_AnnotateWithGene.Level_3.2016012800.0.0	yes