[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
line.
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
>
> [[alternative HTML version deleted]]
>
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