I have reads from 16 conditions, 3 replicates each. I used RSEM to align, so I have TPMs, but I've imported the counts into DESeq2 with tximport so I can normalize the counts and extract DE genes in specific contrasts from the dataset. I have also used DESeq2 to produce batch-corrected variance-stabilized transformations (vst) of the dataset, which produced some nice h-cluster heatmaps, PCA plots, and did k-means clustering. Now, if I want to produce plots that examine the expression of individual genes or clusters, should I plot the DESeq normalized counts or the TPMs, using gene lists derived from the DESeq results? Is it "okay" to define clusters with the vst data and but then show the TPMs? Not sure what standard practice is. Thanks!
Question: Plot normalized counts DESeq or TPM?
22 months ago by
Michael Gallagher • 0 wrote:
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