Metagenome seq errors using biom (1.3) file
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@drrichrodrigues-11249
Last seen 5.1 years ago

Hi

I generated a biom (1.3) file using QIIME (1.8). I am trying to run metagenomeseq in R (biomformat_1.0.2     metagenomeSeq_1.14.2). I can read the biom file but get errors in the following steps. Help appreciated!

> x = read_biom("miseq10/otu_table.fractn0.001.biom")
> ObjData = biom2MRexperiment(x)
> ObjData
MRexperiment (storageMode: environment)
assayData: 79 features, 160 samples 
  element names: counts 
protocolData: none
phenoData: none
featureData
  featureNames: 184451 3957916 ... 259556 (79 total)
  fvarLabels: taxonomy1 taxonomy2 ... taxonomy7 (7 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: 

> obj = cumNorm(ObjData, p = cumNormStatFast(ObjData))
Error in `[<-`(`*tmp*`, leng:(leng - length(smat[[i]]) + 1), i, value = numeric(0)) : 
  subscript out of bounds
> obj = cumNorm(ObjData, p = cumNormStat(ObjData))
Error in cumNormStat(ObjData) : Warning empty sample

metagenomeseq qiime biom • 896 views
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@joseph-nathaniel-paulson-6442
Last seen 4.5 years ago
United States
That error means you have samples without a single positive count. Use the function filterData to filter them out before normalization. On Aug 6, 2016, 1:17 PM, at 1:17 PM, "dr.richrodrigues [bioc]" <noreply@bioconductor.org> wrote: >dr.richrodrigues posted the Question: "Metagenome seq errors using biom >(1.3) file": > >Hi I generated a biom (1.3) file using QIIME (1.8). I am trying to run >metagenomeseq in R (biomformat_1.0.2 metagenomeSeq_1.14.2). I can read >the biom file but get errors in the following steps. Help appreciated! >> x = read_biom("miseq10/otu_table.fractn0.001.biom") > ObjData = >biom2MRexperiment(x) > ObjData MRexperiment (storageMode: >environment) assayData: 79 features, 160 samples element names: counts >protocolData: none phenoData: none featureData featureNames: 184451 >3957916 ... 259556 (79 total) fvarLabels: taxonomy1 taxonomy2 ... >taxonomy7 (7 total) fvarMetadata: labelDescription experimentData: use >'experimentData(object)' Annotation: > obj = cumNorm(ObjData, p = >cumNormStatFast(ObjData)) Error in `[<-`(`*tmp*`, leng:(leng - >length(smat[[i]]) + 1), i, value = numeric(0)) : subscript out of >bounds > obj = cumNorm(ObjData, p = cumNormStat(ObjData)) Error in >cumNormStat(ObjData) : Warning empty sample > >--- >See the full post at: Metagenome seq errors using biom (1.3) file >Replying to this email will post an answer to the question above.
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