[Bioc-devel] Duplicate issue in ELMER get.pair for HNSC data

[ghafarpour]

Hi, 

When I try to analyze HNSC data by ELMER using this pipeline 

TCGA.pipe(disease = "HNSC",analysis = "all", genome = "hg19", cores = 1,
permu.size=10000, Pe=0.001) 

I got this error

Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':
'cg00042263.ENSG00000146556', 'cg00045114.ENSG00000234741',
'cg00055603.ENSG00000162365', 'cg00081439.ENSG00000173876',
'cg00082912.ENSG00000011052', 'cg00082912.ENSG00000243678',
'cg00180909.ENSG00000166984', 'cg00216693.ENSG00000075886',
'cg00216693.ENSG00000173272', 'cg00253248.ENSG00000011052',
'cg00253248.ENSG00000243678', 'cg00263146.ENSG00000183666',
'cg00288376.ENSG00000197978', 'cg00288376.ENSG00000225273',
'cg00379619.ENSG00000105640', 'cg00379713.ENSG00000165478',
'cg00411945.ENSG00000172661', 'cg00432262.ENSG00000136270',
'cg00452252.ENSG00000243716', 'cg00459445.ENSG00000146574',
'cg00460916.ENSG00000262304', 'cg00463746.ENSG00000116678',
'cg00482162.ENSG00000015568', 'cg00522451.ENSG00000169629',
'cg00570580.ENSG00000183054', 'cg00610294.ENSG00000258755',
'cg00611227.ENSG00000146556', 'cg00634968.ENSG00000244067',
'cg00655552.ENSG00000151718', 'cg00664723.ENSG00000183666',
'cg00686132.ENSG00000166984', 'cg00750880.ENSG0000023491 [... truncated]


It is the result of running : 

pair <- get.pair(data = mae.hg19,
                 group.col = group.col,
                 group1 = group1,
                 mode = "unsupervised",
                 group2 = group2,
                 nearGenes = nearGenes,
                 diff.dir = diff.dir,
                 minSubgroupFrac = 0.4, # % of samples to use in to
create groups U/M
                 permu.dir = file.path(dir.out,"permu"),
                 permu.size = 100000, # Please set to 100000 to get
significant results
                 raw.pvalue = 0.05,   
                 Pe = 0.001, # Please set to 0.001 to get significant
results
                 filter.probes = TRUE, # See
preAssociationProbeFiltering function
                 filter.percentage = 0.05,
                 filter.portion = 0.3,
                 dir.out = dir.out,
                 cores = 1,
                 label = diff.dir) 

would you please help me to solve it 

https://support.bioconductor.org/p/115251/
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