We received NGS data from a payed facility which performed differential expression analysis without filtering out low expressing genes (mouse, FC calculated for ~50.000 genes)
Now we re-analyzed the data with two different filters (tried limma and edgeR):
(1) Raw counts > 10 which left us with ~16.000 genes
(2) Raw counts > 100 which left us with ~11.000 genes
The results fit better to what we see in the lab with applying a count filter, but do not differ too much between (1) and (2).
Is the second filter too stringent as in the number of genes left are too little?
I am thinking about publishing here - what is acceptable?
Many thanks for your response in advance guys!!!