[BioC] Normalization questions

Kevin R. Coombes kevin.r.coombes at gmail.com
Fri Sep 24 17:21:46 CEST 2010

  Correlation is not the same as "concordance correlation".

Correlation measures where two data vectors follow some sort of straight 

Concordance measures whether they follow the identity line.

On 9/23/2010 11:50 AM, Sean Davis wrote:
> On Thu, Sep 23, 2010 at 12:44 PM, ANJAN PURKAYASTHA<
> anjan.purkayastha at gmail.com>  wrote:
>> > From reading the literature it seems that calculating the concordance
>> correlation coefficient between two normalized arrays is a good measure of
>> success of the normalization procedure. Is there a Bioconductor package
>> that
>> calculates this?
> Hi, Anjan.  The R cor() function can be used to calculate correlation.
>> Secondly, is there a bioconductor function that identifies outlier spot
>> intensities among replicate arrays?
> This is a little vague.  However, there are numerous packages for quality
> assessment of microarrays.  You might try looking at some of those to see if
> they meet your needs for your experimental setup.
> Sean
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