error in DESeq2 results(dds)
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james • 0
@de0a0546
Last seen 7 weeks ago

I am running into an error my code did not used to encounter. The data I am using ran with this code successfully 4 months ago. Any ideas on how to fix or circumvent this error would be appreciated.

> dds <- DESeqDataSetFromMatrix(countData=mycounts, 
                              colData=metadata, 
                              design=~condition,
                              tidy=TRUE)
> dds <- DESeq(dds)
> res <- results(dds, tidy=TRUE)

Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “DFrame” is not valid for slot ‘elementMetadata’ in an object of class “DESeqResults”; is(value, "DataTable_OR_NULL") is not TRUE
DESeq2 datasetfrommatrix results error • 166 views
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Entering edit mode
@mikelove
Last seen 17 hours ago
United States

These types of errors are nearly always caused by invalid installations, check:

BiocManager::valid()
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Thank you, it still gave me the error after updating 4 of the 5 packages that were out of date. But restarting RStudio removed the error.

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