I am producing right now a strange plot while running the DESeq2 workflow when running the command
lfcShrink on the DESeqDataSet object (after running the
I assume right now that there is an error within my workflow but I can not figure out what the problem. In a nutshell this is what I was running on the dataset:
- import of dataset using
tximport(RSEM result files),
- creation of design matrix using limma,
- creation of DESeqDataSet using the tximport object and the design matrix,
- pre-filtering for low-expressed genes,
- running DESeq function on DESeqDataSet,
- creation of contrast matrix,
- running lfcShrink on the DESeq processed DESeqDataSet.
I can update the code of course but maybe someone has some ideas just based on the plot itself.
Thanks much in advance!
left plot showing
results(object=dds,...), right plot showing
Both plots plotted using