R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_RPPA_preprocess/broadinstitute.org/cancer.genome.analysis/10070/12/Rppa_preprocess.R")
> result <- main("-r/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_DataMergerPipeline/UCEC/22231627/GDAC_RPPA_DataMerger_19558421/UCEC.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt", "-a/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess_annotations/UCEC/20121561/UCEC.antibody_annotation.txt", "-bUCEC", "-c1", "-d2")
> q(save="no")