cummRbund error dealing with cuffdiff results
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4.9 years ago
402374688 ▴ 30

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

When I ran the following commands, errors 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.rep <- MDSplot(genes(cuff),replicates=T)

Error in cmdscale(d, eig = TRUE, k = 2) : NA values not allowed in 'd'

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'

RNA-Seq R software error cummeRbund • 1.5k views