diff --git a/episodes/multi-sample.Rmd b/episodes/multi-sample.Rmd index 888beac..131cb82 100644 --- a/episodes/multi-sample.Rmd +++ b/episodes/multi-sample.Rmd @@ -501,18 +501,26 @@ de.results <- pseudoBulkDGE(summed.filt.subset, :::::::::::::::::::::::::::::::::: challenge -#### Exercise 2: `muscat` +#### Exercise 2: -Test differential expressed genes computed with `muscat` package and check for differences in the results. +Use the `pheatmap` package to create a heatmap of the abundances table. Does it comport with the model results? :::::::::::::: hint +You can just hand `pheatmap()` a matrix as its only argument. It has a million options, but the defaults are usually pretty good. ::::::::::::::::::::::: :::::::::::::: solution -TODO +```{r} +library(pheatmap) + +pheatmap(y.ab$counts) +``` + +The top DA result was a decrease in ExE ectoderm in the tomato condition, which you can sort of see, especially if you `log1p()` the counts or discard rows that show much higher values. ExE ectoderm counts were much higher in samples 8 and 10 compared to 5, 7, and 9. + ::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::