Hi,all:

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 using cummeRbund. It showed warning message like this:

http://www.freeimagehosting.net/t4yzi

Warning messages:

1:

2:

And the volcano plot (http://www.freeimagehosting.net/ot994) 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.

Best, Liye

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 using cummeRbund. It showed warning message like this:

http://www.freeimagehosting.net/t4yzi

Warning messages:

1:

**Removed 24226 rows containing non-finite values (stat_density)**.2:

**Removed 22713 rows containing non-finite values (stat_density)**.And the volcano plot (http://www.freeimagehosting.net/ot994) 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.

Best, Liye

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