Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
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Serge • 0
@f824a3d7
Last seen 16 hours ago
Australia

I am trying to setup DEseq from RangedSummarizedExperiment, and it fails because I cannot find the column for the formula.


load("data/rse_gene.Rdata")
dds <- DESeqDataSet(rse_gene, design = ~some_condition) # some_condition is a random name, it is not in the data.

It fails with:

Error in DESeqDataSet(rse_gene, design = ~some_condition) : 
  all variables in design formula must be columns in colData

With a plain counts file, I add this column after loading to the data.frame and everything works. Do I need to add some_condition to the RangedSummarizedExperiment object?

I have tried this with 3 different rse_gene.Rdata files from recount2 - all have the same issue.

Thx

SRA DESeq2 • 101 views
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Entering edit mode
swbarnes2 ▴ 780
@swbarnes2-14086
Last seen 9 hours ago
San Diego

The documentation says that the input has to be (emphasis mine)

a RangedSummarizedExperiment with columns of variables indicating sample information in colData

So your rse_gene needs to have that colData, and of course you pick a design based on Coldata, just like the warning says.

If for some reason you really want to make the dds object without a design, make design ~ 1.

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