I have 16 samples of bulk-RNA-seq data. There are 4 groups, so 4 samples are in each group. I want to check for outliers in each of the groups, and also get some characteristic estimate for each sample in each group of how much of an outlier it is. I am using
DESeq2. There are threads that I found in
With this one I get a bunch of plots which all look approximately the same.
abline() for some reason is not drawn for me, not sure what is the purpose of it (showing genes outliers? I am not interested in it).
If we look to the official documentation:
assays(dds)[["cooks"]] gives the measures for outliers for each gene and sample, but I need to get it just for each sample in each group. I did a boxplot and it looks like that:
What metrics to use to assess how much of an outlier each sample is in each group? I am a bit confused.