Question: metagenomeSeq error question: error on creation of newMRexperiment
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gravatar for slizo001
9 months ago by
slizo0010
slizo0010 wrote:

Hello all,

I am receiving an error message when running data on metagenomeSeq, the root cause of which I'm unable to trace:

Error in validObject(.Object) : 
  invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featureData
invalid class “MRexperiment” object: 2: featureNames differ between assayData and featureData

In general, this error message likely has something to do with the fact that there is mismatch of features in the two matrix sets that I'm using, one matrix which is a count matrix, and another matrix which is taxonomy. Despite checking (rechecking, and rechecking), that the name and order of features are the same (visually and using XLS match function), I am unable to understand where the issue is. I'm a relative novice R user (have extensive SAS training, and only now getting into R coding) 

My code (#with annotation):

library(metagenomeSeq)

#Load gene count matrix
counts = loadMeta("counts.txt", sep = "\t")
dim(counts$counts)

#Load phenotype data. 
pheno = loadPhenoData("pheno.txt", sep = "\t", tran=TRUE)
ord = match(colnames(counts$counts), rownames(pheno))
pheno = pheno[ord, ]
head(pheno)

#Load taxa matrix
taxa = read.delim("taxa.txt", sep = "\t", stringsAsFactors=FALSE,row.names=1)

#Create MRexperiment:
phenotypeData = AnnotatedDataFrame(pheno)
taxaData = AnnotatedDataFrame(taxa)
frontiers = newMRexperiment(counts$counts,phenoData=phenotypeData, featureData=taxaData)

Example counts data (counts.txt):

Gene Samp 1 Samp 2 Samp 3 Samp 4  Samp 5 Samp 6
100|FR772051.1|FR772051|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT3-DPRIME 0 0 0 29 0 0
101|unknown_id|unknown_name|MLS|23S_rRNA_methyltransferases|ERMA 0 0 0 32 0 0
1034|JQ364968.1|JQ364968|betalactams|Class_A_betalactamases|CARB 0 0 0 0 0 0
105|FR772051.1|FR772051|MLS|ABC_transporter|VGA 0 0 0 0 0 0
1090|DQ303459.3|DQ303459|betalactams|Class_A_betalactamases|CTX 0 0 0 0 0 377
1119|M55547.1|TRNTAAB|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT3-DPRIME 0 0 0 0 0 0
1205|JN086160.1|JN086160|MLS|23S_rRNA_methyltransferases|ERMF 0 0 0 0 0 0
122|AJ579365.1|AJ579365|MLS|Streptogramin_resistance_ATP-binding_cassette_ABC_efflux_pumps|LSA 0 0 0 0 0 0
126|AJ579365.1|AJ579365|MLS|23S_rRNA_methyltransferases|ERMA 0 0 0 0 0 0
1261|AY178993.1|AY178993|betalactams|Class_A_betalactamases|CARB 0 0 0 0 0 0
1268|AB976602.1|AB976602|betalactams|Class_A_betalactamases|CTX 0 0 0 0 0 0
1374|DQ077487.1|DQ077487|Tetracyclines|Tetracycline_resistance_major_facilitator_superfamily_MFS_efflux_pumps|TET33 0 0 0 0 0 0
1390|EU348758.1|EU348758|MLS|23S_rRNA_methyltransferases|ERMA 0 0 0 0 0 0
143|unknown_id|unknown_name|Tetracyclines|Tetracycline_transcriptional_repressor|TETR|RequiresSNPConfirmation 0 0 0 0 0 0

Example taxa data (taxa.txt):

 

Gene Trait
100|FR772051.1|FR772051|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT3-DPRIME AMR
101|unknown_id|unknown_name|MLS|23S_rRNA_methyltransferases|ERMA AMR
1034|JQ364968.1|JQ364968|betalactams|Class_A_betalactamases|CARB AMR
105|FR772051.1|FR772051|MLS|ABC_transporter|VGA AMR
1090|DQ303459.3|DQ303459|betalactams|Class_A_betalactamases|CTX AMR
1119|M55547.1|TRNTAAB|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT3-DPRIME AMR
1205|JN086160.1|JN086160|MLS|23S_rRNA_methyltransferases|ERMF AMR
122|AJ579365.1|AJ579365|MLS|Streptogramin_resistance_ATP-binding_cassette_ABC_efflux_pumps|LSA AMR
126|AJ579365.1|AJ579365|MLS|23S_rRNA_methyltransferases|ERMA AMR
1261|AY178993.1|AY178993|betalactams|Class_A_betalactamases|CARB AMR
1268|AB976602.1|AB976602|betalactams|Class_A_betalactamases|CTX AMR
1374|DQ077487.1|DQ077487|Tetracyclines|Tetracycline_resistance_major_facilitator_superfamily_MFS_efflux_pumps|TET33 AMR
1390|EU348758.1|EU348758|MLS|23S_rRNA_methyltransferases|ERMA AMR
143|unknown_id|unknown_name|Tetracyclines|Tetracycline_transcriptional_repressor|TETR|RequiresSNPConfirmation AMR

 

The error occurs when running the last line of script: frontiers = newMRexperiment(counts$counts,phenoData=phenotypeData, featureData=taxaData)

Is there an obvious mistake here that I'm just not seeing? Very grateful for your time and help in addressing this dilemma.-IS

ADD COMMENTlink written 9 months ago by slizo0010
Have you checked that taxa is of the right dimensions and with the same row names as in `counts$counts`?
ADD REPLYlink written 9 months ago by Lluís Revilla Sancho500
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