After I ran cuffdiff and got the DE results, I was trying to visualize the results with cummeRbund package.

When I ran the following command, an error occurred. Typically it was normal and worked well without the replicates=T parameter, but when added some errors just came out. How can I fix this? Thank you.

> genes.MDS <- MDSplot(genes(cuff))
> genes.MDS
> genes.MDS.rep <- MDSplot(genes(cuff),replicates=T)
Error in cmdscale(d, eig = TRUE, k = 2) : NA values not allowed in 'd'

and also:

> csDistHeat(genes(cuff))
Warning message:
Non Lab interpolation is deprecated 
> csDistHeat(genes(cuff),replicates=T)
Error in hclust(obj.dists) : NaN dissimilarity value.

> genes.PCA.rep<-PCAplot(genes(cuff),"PC1","PC2",replicates=T)
Error in svd(x, nu = 0) : infinite or missing values in 'x'