Count cuttoff for Diff expression DESeq and Cufflinks/Cuffdiff

[rspitale]

Hey All,

This is my first post, so please bear with me.

I have been doing differential expression with DESeq and Cuffdiff.

I just wondered at what level do people usually exclude genes from analysis.

For example in DEseq, what number of raw counts do you exclude (i.e.- 10 and up, etc)?

For Cuffdiff, what level do you cut off RPKM/FPKM. (i.e.- 1 and above use for differntial expression)?

Also, for multiple samples do you sort all sample types by expression and remove all genes for each sample at that value?

Sorry if this is confusing. Thanks!