hello all,
I calculated correlation by this function for control and tumor:
control.corr=cor(cod[grep(".C",cod$name),-1],nc[grep(".C",nc$name),-1],method = "spearman") tumor.corr=cor(cod[grep(".T",cod$name),-1],nc[grep(".T",nc$name),-1],method = "spearman")
so I have two matrix of r pairwise, now I want calculate p-value for the r's, what should I do?
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Edalat •
1 answer
control.corrP=cor.test(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method = "spearman")$p.value
Error in cor.test.default(coding.rpkm[grep("23.C", coding.rpkm$name), : 'x' and 'y' must have the same length
there is an error,why? it is clear that the number of coding and ncoding are not same.
I think in your case correlation analysis will not be meaningful. I can suggest t-test or Kruskal Wallis statistics.
Note: if you have more number of samples (example 10), you can use correlation of individual coding and noncoding expression with respect to 10 samples ( this will make sense because you will have same number of samples in both case).
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