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Old 06-19-2015, 05:27 PM   #1
bugbitten
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Location: South San Francisco

Join Date: Jun 2015
Posts: 3
Default Error in microbial count object: Error in hatmatrix/non-conformable arguments

I imported a phyloseq object to DESEQ2 for obtaining the log2fold change in the number of OTU's per sample. My condition is the disease_stat: cancer, healthy, adenoma

Following is the code i used:

phyloseq_to_deseq2(biom_otu_tax, ~disease_stat)
cts=counts(DESeq2BIOM)
geoMeans = apply(cts, 1, function(row) if (all(row == 0)) 0 else exp(mean(log(row[row != 0]))))
DESeq2BIOM = estimateSizeFactors(DESeq2BIOM, geoMeans = geoMeans)
#It stopped working after this point
DESeq2BIOM = estimateDispersions(DESeq2BIOM)
DESeq2BIOMRES = DESeq(DESeq2BIOM,test = "Wald", betaPrior = "FALSE")
DESeq2BIOMRES = DESeq(DESeq2BIOM,test = "Wald")

The error I get is Error in t(hatmatrix %*% t(y)) :
"error in evaluating the argument 'x' in selecting a method for function 't': Error in hatmatrix %*% t(y) : non-conformable arguments"

I browsed a few other solutions before posting a question: http://seqanswers.com/forums/archive...p/t-46009.html
They did not address my issue.

What does this error indicate? Help in troubleshooting much appreciated!
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