[R] correlating between two vectors of numbers

Sean Davis sdavis2 at mail.nih.gov
Thu Oct 14 14:53:24 CEST 2004


Anders,

Does your data have missing values?  It looks like they might.   Look 
at the 'use' parameter in cor.  Also, is there a reason to use cor.test 
instead of cor.  Finally, if the expression values are not normal, 
could you transform them first to make them more so--log2, for example? 
  And, no, no one has figured out the "best" way to define 
distances/correlations for microarray, at least to the best of my 
knowledge.

Sean

On Oct 14, 2004, at 8:37 AM, Anders Stegmann wrote:

> Hi, R!
>
>
>
> Question1:
>
> I am trying to correlate two vectors of numbers (two columns of 
> microarray
> signal values) by using the non-parametric Spearman's rank correlation
> coefficient rho:
>
>> cor.test(V2.Signal,V3.Signal,method="spearman")
>
> but I get the error message:
>
> Error in if (q > (n^3 - n)/6) pspearman(q - 1, n, lower.tail = FALSE) 
> else
> pspearman(q,  :
>         missing value where logical needed
> In addition: Warning message:
> NAs introduced by coercion
>
> I have tried to use the parametric Pearson correlation and the
> non-parametric Kendall's tau correlation and had no problem with that!!
>
>> cor(V2.Signal,V3.Signal,use="complete.obs")                        
>> (the
> Pearson correlation)
>
>> cor.test(V2.Signal,V3.Signal,method="kendall")                     
>> (the
> Kendall's correlation)
>
>
> what's wrong?
>
>
>
> Question2:
>
> Does anyone accidently know which correlation method would be the most
> correct to use when the microarray signal values (the values to be
> correlated) are not normal distributed (the Kendall's method seem to 
> fit
> better to my other tests than the Pearson method).
>
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