[BioC] duplicate cor?
Jianping Jin
jjin at email.unc.edu
Thu Feb 23 19:14:53 CET 2006
Dear Bioconductor list:
Could anyone provide a good explanation on "duplicateCorrelaton"? There are
two one-channel non-Affymetrix data sets in each of which each gene was
spotted twice on each chip. To estimate correlation between duplicate
values, I ran regular cor.test for each gene across all chips. The results
showed average cor values as 0.52 and 0.81 for the two sets respectively.
The $consensus.correlation after running "duplicateCorrelation" was shown,
however, at opposite direction: 0.57 and 0.27 (even negative in some other
cases). I was told once that duplicateCorrelation is the residual
correlation. But I have no idea of how to coordinate two into a clear
picture. We know the lower is residue the better the data are correlated
(more consistent). Does this hold on residue correlation compared to total
correlation as well?
The on-line document on duplicateCorrelation said "consensus correlation is
the trimmed mean of the individual correlations on the atanh-transformed
scale". I don't know what is the atanh scale. But is it related to where I
misunderstood the consensus correlation?
Thanks in advance!
Jianping
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