Hi guys, I have a question about how to define a gene to be expressed in RNA Seq analysis.
Is it better to use log2(rpkm) or rpkm without log2 transformation to define a gene to be expressed? I know that the log is only a transformation so that log2(rpkm) will let to consider as expressed a gene with a higher rpkm with respect to the simple rpkm. However I think that rpkm alone leads to consider as expressed genes that have too few reads.

Some ideas about? 

Thank you in advance
If you just want to filter out genes of low expression prior to performing downstream analyses, then just go by the RPKM values and eliminate genes with mean RPKM < 10 or < 20, and / or those genes with a high frequency of 0 or NA values.

If your aim, however, is to define, for example, an expression signature for a particular tissue or condition, then transform your RPKM dataset to Z-scores via *zFPKM* package (R Programming Language) and then set cut-offs:

 - Z > 2 = expressed
 - Z < -2 = not expressed

Those cut-offs can, of course, be modified.

Note that neither RPKM, FPKM, nor CPM data is suitable for differential expression analysis, and neither are the logged transformations of these.

Kevin