Question: Hierarchical Clustering of copy number variations
0
gravatar for kulani.s91
23 months ago by
kulani.s910
kulani.s910 wrote:

I have a dataset of CNA of genes

GENE X1 X2 X3 X4 X5
TP53 0  1  0  0  -2
PTEN 0  0 -1  0  0
AR   NA NA NA NA NA

When I run the code,

> mRNA_Data_hclust <- dist(test, method='euclidean') 
> mRNA_hclust <- hclust(mRNA_Data_hclust, method = "complete")

I get the following error.

Error in hclust(mRNA_Data_hclust, method = "complete") : 
  NA/NaN/Inf in foreign function call (arg 11)

How do I handle the error without removing the NA values?

R software error • 643 views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 23 months ago by kulani.s910
1

Why not just remove NA values?

ADD REPLYlink written 23 months ago by Sean Davis25k

CNA from RNA data has been done in the past, but is very challenging

You could use impute() to cover up NAs. but that will not help with entire rows of NAs

ADD REPLYlink written 23 months ago by Jan Oosting910

Important to understand why something is NA, in this case. You ave other values that are 0, which indicates unchanged, i.e., normal copy number. What's the difference between NA and 0 in your data?

I think that the ideal solution is to investigate what leads to a NA being assigned.

ADD REPLYlink written 21 months ago by Kevin Blighe54k
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