Hello Everyone,
I'm looking to run something similar to a plotCount on my RNA-seq samples, but I'm interested in showing how a certain gene list (that I determined through analyzing publicly available datasets) is expressed in one condition over another. I know plotCount doesn't have the ability to plot more than one gene, but even so I think using the normalized read counts wouldn't work well because we can have a variety in the expression level (as determined by the count) but a different in the differential expression between one sample over the other.
I know we can adjust the normalized values to a z score when plotting a heatmap using pheatmap (see https://hbctraining.github.io/DGE_workshop/lessons/06_DGE_visualizing_results.html), but I was wondering if we can apply this to plotCounts and visually see the expression profile of the gene list in the different samples.
Is this something that can be done?
Thank you in advance,
Yonatan
DESeq2's PlotCounts is just a little wrapper around a ggplot2 call. You aren't married to it. Just learn how to do ggplot.
need further clarification in order to help.