Duplicate issue in ELMER get.pair for HNSC data
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ghafarpour • 0
@ghafarpour-18385
Last seen 2.4 years ago

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

 

HNSC ELMER • 294 views
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Please, which ELMER version is installed ? 

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latest version (v2)

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There was some genes that had different entrezid for the same emsembleID. I commit a fix to consider that case. 

Please, could you reinstall from github with:

devtools::install_github("tiagochst/ELMER")
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