plots in deseq2 #32
Description
Hi,
First, totally new to rnaseq analysis... figured out the command line portion (star, stringtie) and also managed deseq2 in R.
So I figured out how to analyze the differential expression in R, got actual fold change values in the command line tables!! But... I can't figure out how to 'save' the resulting expression analysis as a csv file. I did this below but I have no idea where the file is; I checked all of the folders, don't see it.
write.table(res, file="ctrlVS10um.txt", append = FALSE, sep = "\t" )
The other issue is when I tried plotMA or plotcounts, it looks like its running, but I have no idea where to find the graphs. Is it supposed to pop up in my command line window? How would I find the graphs so I can save and export them onto my local computer?
I've been googling both, but all I find are instructions on how to generate graphs or save files, nothing on how to actually save them or where they go.
Thank you.