I have been trying to run a PCA on some RNA-seq data I have obtained through Salmon, but for some reason, when I put the appropriate command into RStudio, I don't get any response. I made a DESeq2 dataset (named dds, as in the tutorial) using the typical commands, then transformed the data using the rlog command:
rld <- rlog(dds, blind=TRUE)
And used this transformed data for the plotPCA function:
Where "Special.Condition" is a column in my coldata file.
After about 5 seconds of running, the function finishes and does not create any plot or new file in my environment. Does anybody know if there is an issue with my code, or could this be a problem with RStudio itself? Thanks, Krzysztof.