how to visualize the distribution of 20,000 genes in gene expression data
Hi,
I need to visualize the distribution of 20,000 genes for 1000 patients in gene expression data to see how far it is from Normal distribution assumption , to perform an eQTL analysis to see if the transformation of log is meaningful ( no bimodal plots)
Can anyone suggest how to visualize the distribution of 20,000 genes
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Why not just use plot() for each gene?
is this an efficient way to see all plots at once , so I have 20,000 plot ??!
I don't know if you're better off heatmapping a quarter million data points though, especially if you're not scaling the data for each gene. Maybe visual examination is out of the question. Instead iterate through each gene, and do a shapiro test for each to assess normality:
Combine these pvalues into a list for all of your genes, and sort by pvalue. Anything significant is a normal distribution.