Question: cummeRbund error dealing with cuffdiff results
gravatar for wastdc
21 months ago by
wastdc0 wrote:

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'



ADD COMMENTlink modified 21 months ago • written 21 months ago by wastdc0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 191 users visited in the last hour