[BioC] correlation coefficient for microarray biological replicates

[Wolfgang Huber]

Dear Barbara

both are actually not very useful for this purpose (and, as Sean said, 
in about equal measure). For one alternative, have a look at the 'idr' 
package on CRAN and this paper:
Q. Li, J. B. Brown, H. Huang and P. J. Bickel (2011). Measuring 
reproducibility of high-throughput experiments. Annals of Applied 
Statistics. www.stat.berkeley.edu/tech-reports/790.pdf

	Best wishes
	Wolfgang



Jul/23/12 4:17 PM, Sean Davis scripsit::
> On Mon, Jul 23, 2012 at 7:58 AM, Barbara Uszczynska <uszczynska at gmail.com>wrote:
>
>> Dear Conductors,
>>
>> Is it better to use Pearson's or Spearman's correlation coefficient to
>> measure the reproducibility among microarray biological replicates?
>>
>> I would be grateful for any hint.
>>
>>
> Typically, after normalization, they will be nearly the same since the
> effect of normalization is often to make the distributions of the arrays
> similar.
>
> Sean
>
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>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber