Hello!

I am using limma with the voomWithQualityWeights functionality and have had no problems with any errors. I was really just wondering if there was a way to utilize the voom weighted and normalized counts so that I can make a heatmap of expression? I was able to do this with the cmp() function for the raw counts matrix but have not been able to figure out how to do it for the counts with the weights applied.

Any ideas would be great!

Heatmaps have no way to use precision weights, so the voom output is no help to produce a heatmap. That's why we recommend you use the cpm() function to make descriptive plots like this. The prior.count used in the cpm() function damps down the variability of the low counts, which is somewhat analogous to the downweighting that the voom precision weights do in a linear model.

You also ask about quality weights, but there is no way to normalize out sample quality weights.