Linear Regression Diagnostic Plots with DESeq2
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@aaronbuechlein-14296
Last seen 16 days ago

Is there a way to create simple diagnostic plots from the DESeqDataSet object, plots similar to simply plot(fit) where fit is an lm object? Basically plots similar to this https://data.library.virginia.edu/diagnostic-plots/. I've dug around the DESeqDataSet object, but can't find the information I need.

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@mikelove
Last seen 12 hours ago
United States

Short answer is no.

We do provide the mean values "mu" and the hat matrix diagonals "H" in assays(dds), so you could make your own GLM diagnostic plots if you want.

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

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