HI Dr. Smyth,

I am trying to find the appropriate mRNA expression level estimates to use for generating plots that demonstrate the differential expression statistics calculated from voom/limma. What do you recommend? FPKM plots don't always agree with my voom/limma results.

For example, if the differential expression results from limma report a log Fold change of 2 for group A vs. group B, I want a plot (e.g. boxplot, bar graph, etc.) which visualizes this difference and also provides a realistic estimate of the expression level along the axis.

If you have other types of visualization (or normalizations) that you prefer for showing estimated expression levels between groups that also demonstrate the limma differential expression trends, please share. I'm open to any ideas/suggestions that you have.

Thanks,
Heather


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