caculate correlation
Hi Elham, Without knowing much about what coding.rpkm and ncoding.rkpm look like, it is difficult to say. Have you tried to subset these matrices as you do in the "cor" function and see what is returned? Jim On Tue, Jan 31, 2017 at 6:40 AM, Elham - via R-help
<r-help at r-project.org> wrote:
for calculating correlation between coding and noncoding,first I transposed data ,(rows become columns) so row is control&treatment and columns are gene names.(so I have 2 matrix with same row and different column),I use these function for calculating correlation but all of spearman correlation are NA,why?
control.corr=cor(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method= "spearman")
tumor.corr=cor(coding.rpkm [grep("27.T", coding.rpkm $name),-1], ncoding.rpkm [grep("27.T", ncoding.rpkm $name),-1],method = "spearman")
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