Heya,

In advance, apologies if the answer to this question is elementary or easy. But I'm quite new to this whole bioinformatics thing and R in general and recently started using the DESeq2 package on my supervisor's advice. I have an RNAseq matrix consisting of raw counts of my genes of interest with IDs attached and some sample information. I turned my data succesfully into a DESeqDataSet and I have already managed to do differential gene expression analysis using my variable of interest.

Now I want to rlog transform my raw counts using DESeq2 and export them back to a normal R data frame so I can do some further analyses on the transformed data outside of DESeq.

I have searched through all the vignettes and information about DESeq2 exportation and the rlog function and also the forums but I have yet to find an answer.

I hope any of you veterans is willing to help me with this. I would greatly appreciate it if I could get this working.

Thanks in advance!