Question: Duplicate issue in ELMER get.pair for HNSC data
gravatar for ghafarpour
22 days ago by
ghafarpour0 wrote:

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


ADD COMMENTlink written 22 days ago by ghafarpour0

Please, which ELMER version is installed ? 

ADD REPLYlink written 21 days ago by Tiago Chedraoui Silva150

latest version (v2)

ADD REPLYlink written 21 days ago by ghafarpour0

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:

ADD REPLYlink written 20 days ago by Tiago Chedraoui Silva150
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