Retrieving information from boxplots in R
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5 weeks ago
BlueSky ▴ 10

I've tried plotting the boxplot from the code in another post "Box plot for rna seq data" where geom_boxplot() is used to visualise the differences in gene expression between two different groups. However I have a question: If you had 200 genes or more that you would like to compare between the two groups (which is too much to visualise on a plot), how can you get the values that tells you if one group has a significantly differing median than the other group? When you have fewer genes, you can just manually look at if the notches don't overlap between the two groups. And also how to find which of the group that has the higher expression value compared to the other group when not manually looking at the plot? I'm new in R, sorry if this is a basic question.

median geom_boxplot significance notches • 161 views
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You should probably run differential expression analysis with your whole dataset. See the edgeR or DESeq2 documentation.

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I have done that between the samples from sick individuals and healthy controls, but the problem now is that I have divided the sick samples into further groups which I like to explore the difference in expression of. Do you mean that I shall run a new differential expression for these groups?

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