DESeq2 error - converting result object into dataframe

Question

[shasabhi1]

Hello everyone,

I am performing differential expression analysis using DESeq2 and the results contrasts as follows:

res <- as.data.frame(results(dds, contrast=c(Var, effectvar, baselinevar), alpha = as.numeric(pvalue)))
res <- res[order(res$padj), ]
res$ensembl_gene_id <- rownames(res)
rownames(res) <- NULL
res <- na.omit(res)
res_all <- res

This has worked before but now it is giving the error:

Warning: Error in auto_copy: `x` and `y` must share the same src.
 `x` is a <data.frame> object.
 `y` is `NULL`.
 Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be slow).
  3: runApp
  2: print.shiny.appobj
  1: <Anonymous>

I haven't seen any solutions to this and I don't know why this error occurred - I primarily want to convert the DESeq2 results object into a dataframe. I have verified that the input values belong to the correct classes and are embedded correctly.

Any suggestions would be appreciated!

[Ram]

You're not just performing DE analysis, you're using shiny. This looks like a shiny error, not a DESeq2 error.