Deseq2 count matrix

Question

[Sam]

Hi all

I have raw reads matrix for miRNAs expression and I want complete the differential expression analysis with DESeq2, how I can exclude reads with average reads below 1 (average reads of biological replicates) from count matrix before analysis with Deseq2 ?

Thanks

[ATpoint]

You do not need to. DESeq2 has an internal data-driven function to exclude low counts. There are many questions/posts about this topic on Bioconductor, just google around a bit.

[Sam]

is it also exclude samples have zero counts ? I find this comment in bioconductor for NA p-value

"Note on p-values set to NA: some values in the results table can be set to NA for one of the following reasons:

If within a row, all samples have zero counts, the baseMean column will be zero, and the log2 fold change estimates, p value and adjusted p value will all be set to NA."

[Kevin Blighe]

You will have to specifically remove transcripts with 0 counts, as DESeq2 will leave these in the dataset and not do anything with them. Take a look at Michael Love's answer here: https://support.bioconductor.org/p/64153/

If you want to filter your results() object from DEseq2, then take a look at Michael Love's answer here: https://support.bioconductor.org/p/96219/