Question: Affinity Propagation on copy number alteration data
0
gravatar for kulani.s91
2.5 years ago by
kulani.s910
kulani.s910 wrote:
GENE_ID X53 X54 X56 X57
ALK      0   0   1   1
APC      0   0   0   0
AR       2   2   0   2
ASXL1    0   1  -1   0
ATRX     0  -1   1  -1

I have the dataset above. I used the R code

> test <- read.table("test.csv", sep=",", header = TRUE, fill = TRUE)
> test <- as.matrix(test)
> apres5 <- apcluster(negDistMat(r=2), test, q=0, details=TRUE)
> plot(apres5, test)
> heatmap(apres5)

I get the following error when I run the code

> plot(apres5, test)
Error in .local(x, y, ...) : cannot plot more than 15 features at once
> heatmap(apres5)
Error in rep(sideColors, sapply(x@clusters[[x@maxNoClusters]][srtIndex],  : 
  invalid 'times' argument
In addition: Warning message:
In .local(s, x, ...) : there is nothing to cluster

Any idea how to resolve this?

R software error • 635 views
ADD COMMENTlink written 2.5 years ago by kulani.s910
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