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Question: DEXSeq throws a warning - rank-deficient matrix
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gravatar for Assa Yeroslaviz
9 months ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

Hi,

I am using dexseq to analyse some mouse data and get the following warnings. I know they are just warnings, but would like to understand what it means

Fit for gene/exon ENSMUSG00000017286+ENSMUSG00000049396+ENSMUSG00000017288 threw the next warning(s): the matrix is either rank-deficient or indefinite 
Fit for gene/exon ENSMUSG00000018581 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000023084+ENSMUSG00000028073 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000090266+ENSMUSG00000020818 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000040936 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000030303 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000030303 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSMUSG00000030303 threw the next warning(s): the matrix is either rank-deficient or indefinite

In total I have 145 rows (=exons?) with NA in both the is.na(mcols(dxd1)$log2fold_ES_EB2) & !is.na(DEXSeqResults(dxd1)$padj)

Thanks

Assa

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