CummeRbund plots come out in a different way than they are in the Nature protocol

[rumeys]

Hi everyone,
I am trying to complete the procedure in the Nature Protocol Paper (Differential gene and transcript expression analysis of RNA-seq experiments with Tophat and Cufflinks, by Trapnell et al.)

The thing is that my CummeRbund plots are not similar with those in the paper. For example, the attached density plot is very different than expected. You may observe the graphs(density, scatter and volcano) in the attached pdf.

What can I do now? Does anyone have a suggestion?

The R commands are written as in the protocol.
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
csScatter(genes(cuff_data), 'C1', 'C2')
csVolcano(genes(cuff_data), 'C1', 'C2')

In the linux terminal, after executing csDensity(genes(cuff_data)) command, it gave warning messages:
1: Removed 25 rows containing non-finite values (stat_density)
2: Removed 25 rows containing non-finite values (stat_density)

The reason for being different can be this removal of rows? I'm using R version 3.2.1.

Also, there is a removal of 6 rows after the execution of volcano plot.
Warning message: Removed 6 rows containing missing values (geom_point)

I'd be appreciated for any comments. Thank you!