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Problem With Data Containing Non-Finite Values In Cummerund Processing

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 (density plot) using cummeRbund. It showed warning message like this:

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 (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.

Best, Liye

cufflinks rna-seq
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written by Liye Zhang Liye Zhang

1 answer

Hi, I got an answer from Seqanswers forum. Just quote it in here, in case you are interested.

from "Blanco"

" I believe this is caused by fpkm values of zero. When the program takes the log of zero it becomes minus infinite (-Inf) and these values are excluded from the analysis. I think there is an option called "pseudocount=0.0001" which adds 0.0001 to all zero values to work around this and keep all values in the analysis. If you do that the density should pile up close to the y-axis. Not sure if that is what you would want but it is an option. I tend to think it is ok to discard the zero fpkm values. "

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written by Liye Zhang Liye Zhang

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