is it possible to save the plot in another directory?

[hfl112]

I didn't find a parameter to save it in another location

And another problem is , if I have no down-reg genes, it always have a error infomation to let me change the cutoff, is it possible to just leave it blank in either up- or down-reg?

[reneshbedre]

By default, plots will be saved in the current directory. Maybe you can write a wrapper script to move the files in your destination directory.

If you have no downregulated genes with a given cut-off. You can always change threshold parameters (log fold change and/or p-value)