Pre-filtering in DESeq2 vignette

Question

[dylannicoembros]

I am doing a pre-filtering of my counts following deseq2 vignette:

https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

In the section Pre-filtering they select the significant counts (>= 10), but I cannot understand what is the SmallestGroupSize variable. It refers to the smallest group size of reads for each sample ? how can I check the number ?

Answer 1

[ATpoint]

It's the number of samples in the smallest group in the design. If you habe three groups, say cancer, metastasis and normal with sample size 10, 5 and three then smallest group is three. I personally prefer filterByExpr from edgeR because it is automated, group-aware and well stood the test of time.

[dylannicoembros]

Thank you for the answer.