Question: Syntax of DESeq2 contrast argument for all pairwise comparisons
0
gravatar for natalie.hull
2.5 years ago by
natalie.hull0 wrote:

I'm trying to use DESeq2 to determine if an OTU is enriched by treatments from 16S rRNA sequence data.  I imported OTU counts for each library (otu), and metadata information for each library (meta).  One of my metadata columns is a factor with 5 levels (factors).  I want to do all pairwise comparisons for all 5 factor levels.

 

I've tried to do it this way:

dds = DESeqDataSetFromMatrix(countData = otu, colData = meta, design = ~factors, betaPrior = FALSE)

The rownames in my metadata are the same as the colnames in the otu table, but I get an error:

Error in FUN(X[[i]], ...) :   assay colnames() must be NULL or equal colData rownames()

 

I also tried using phyloseq this way:

dds = phyloseq_to_deseq2(phyloseq(otu,meta), design = ~factors)

dds = DESeq(dds, design = ~ factors)

This method only compared the first and last factor levels, but I want all the comparisons.

 

I need help with the syntax for the contrast argument.

Thanks!

 

deseq2 contrast matrix • 498 views
ADD COMMENTlink modified 2.5 years ago by Michael Love25k • written 2.5 years ago by natalie.hull0
Answer: Syntax of DESeq2 contrast argument for all pairwise comparisons
0
gravatar for Michael Love
2.5 years ago by
Michael Love25k
United States
Michael Love25k wrote:
"rownames in my metadata are the same as the colnames in the otu table" Can you show that this is the case? That is what the error is coming from, SummarizedExperiment found a mismatch.
ADD COMMENTlink written 2.5 years ago by Michael Love25k
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