Question: Duplicate issue in ELMER get.pair for HNSC data
0
gravatar for ghafarpour
10 months ago by
ghafarpour0
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

 

elmer hnsc • 205 views
ADD COMMENTlink written 10 months ago by ghafarpour0

Please, which ELMER version is installed ? 

ADD REPLYlink written 10 months ago by Tiago Chedraoui Silva240

latest version (v2)

ADD REPLYlink written 10 months 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:

devtools::install_github("tiagochst/ELMER")
ADD REPLYlink written 10 months ago by Tiago Chedraoui Silva240
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