I have a very quick question for my own sanity to check this is ok.

The vignette for DESeq2 states that the 'function DESeqDataSetFromMatrix can be used if you already have a matrix of read counts prepared from another source.'

This perfectly clear and fine, however i would like to confirm that the input of a counts matrix as a dataframe is also a valid input.

Reading in the counts table as a data frame where columns are samples and rows are ensembl IDs works fine for me as an input to the countData argument in DESeqDataSetFromMatrix.. and the further PCA and DE analysis makes perfect sense between samples, but just making sure that a data frame input should indeed produce the same result as if the counts table were a class(matrix).

thanks!

Yes, a data.frame of counts is converted to matrix internally.