Is there a way to make a heatmap using DESeq2 for paired data? I am comparing the lung microbiome with the mouth microbiome in 33 patients And also comparing the lung microbiome over two time points (again paired data).
My OTU table was loaded into R:
and my sort of "map" file which just contains SampleID, Location, and Paired. For example:
SampleID Location Paired
1_L Lung 1
1_M Mouth 1
2_L Lung 2
2_M Mouth 2
map=read.csv('C:\Users\OneDrive\Mouth vs lung R map_adj.csv',header=T,row.name=1,stringsAsFactors=F)
Again my data is paired and I want to compare the lung vs the mouth (location) using a heatmap. I've been having trouble with R. And then again with time (baseline vs later) (baseline vs x number of months later).