Which correlation coefficient is best to compute the correlation of two genes in cancer tissues among Pearson, Spearman and Kendall. I already analyzed with Pearson correlation coefficient. Please let men know If it is good how can I justify for selecting Pearson coefficient.
1 answer
A general rule of thumb for any correlation:
Pearson
- parametric
- 'large' (representative) sample size
- data follows a normal distribution
- data is typically continuous
On the last point, if one conducts a linear regression where the predictor is a factor, it's the exact same as performing a Pearson correlation where that same factor is encoded numerically - see A: In GSEA, how can one "correlate" gene expression with categorical phenotype data
In an RNA-seq context, 'large' can simply mean a study comprising 5 biological replicates (some would say 3).
Kendall | Spearman rank correlation
- non-parametric
- small or large (i.e. any) sample size
- skewed data / data does not follow normal distrubtion
- ordinal or continuous data
Kevin
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