Question: metagenomeSeq error question: error on creation of newMRexperiment
0
6 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)

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, ]

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

#Create MRexperiment:
phenotypeData = AnnotatedDataFrame(pheno)
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

Have you checked that taxa is of the right dimensions and with the same row names as in counts\$counts?