Entering edit mode
6.9 years ago
anu014
▴
190
Hello Biostars,
I am doing MDSplot like this :
library(cummeRbund)
cuff<-readCufflinks(gtfFile="merged.gtf",genome="grch38")
cuff
CuffSet instance with:
2 samples
56875 genes
282953 isoforms
131485 TSS
81720 CDS
56875 promoters
131485 splicing
18767 relCDS
try(genes.MDS<-MDSplot(genes(cuff)))
But it's throwing this error :
Error in cmdscale(d, eig = TRUE, k = 2) : 'k' must be in {1, 2, .. n - 1} Error in try(genes.MDS) : object 'genes.MDS' not found
How can I fix this error? Please help.. Thanks in advance :)
I am not a huge expert on cummeRbund, but it looks like you first extract the genes from
cuff
object, then you use them to create MDS-plot. Usually, the input for MDS (or PCA) is some rectangular data, e.g. genes in rows, samples in columns. For me it looks like you are using just "genes". Am I right?