I have the transcriptome of three different cell types (e.g. macrophages, neurons and T cells) and I am looking to evaluate tissue specific gene expression across these three cell types. For example, mpeg1 is a macrophage specific gene and therefore I see its expression enriched in macrophages and not in the other cells when I compare the normalized reads expression. Is this comparison of normalized reads count enough to compare/claim tissue specific gene expression? I have more than 3 biological replicates per condition and sequencing depth of more than 50 M reads per sample. I have been just plotting normalized reads from DESeq2 and just doing a 2-way anova with multiple comparison test (tukey) to do statistics.
I understand that since DE analysis is a pair-wise comparison only, is there a better way to go about this analysis? I am looking to plot the results and get an statistical test without having to do DGE for all the comparisons possible (3 cell types against each other).
Thanks in advance, Margot