Hi all,
I have a dataset from a single cell RNASeq project and there are many genes with very few counts (1 or 2 in a few samples) in the data set. While this is important info (tells us that these genes are not expressed), how would one handle them for a differential expression analysis (I use DESeq2)? Should I delete them or keep them? For me this means the difference between having a dataset with either ~17000 genes or ~11,500 genes (if I exclude genes with an average count less than 3).
Thanks for your thoughts on this!
I have a dataset from a single cell RNASeq project and there are many genes with very few counts (1 or 2 in a few samples) in the data set. While this is important info (tells us that these genes are not expressed), how would one handle them for a differential expression analysis (I use DESeq2)? Should I delete them or keep them? For me this means the difference between having a dataset with either ~17000 genes or ~11,500 genes (if I exclude genes with an average count less than 3).
Thanks for your thoughts on this!
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