Recently, I am trying to identify the differentially expressed genes between two conditions. Each condition has three replicates(paired end). I got a problem when I am trying to analyze the data using Tophat v2.0.4, Cufflinks v2.0.2 and cummeRbund v2.0.0.
The problem is that when I try to generate the density plot (density plot) using cummeRbund. It showed warning message like this:
1: Removed 24226 rows containing non-finite values (stat_density).
2: Removed 22713 rows containing non-finite values (stat_density).
And the volcano plot (volcano plot) also did not seem to be right. I am not clear the cause of non-finite values in my dataset and why there are so many of them have this problem.
I suspect that this is because I use "--compatible-hits-norm" normalization parameter in cufflinks. I just wonder whether you have some experience on this and any suggestions will be greatly appreciated.