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I have 4 arrays in technical replicate dyeswap pairs. Using
duplicateCorrelation (LIMMA) I got a positive correlation for the
consensus
correlation and I cannot understand how this is possible. There is
really
no evidence of dye-bias. But 13% of the noncontrol spots have
correlation
higher than 0.9. I have done extensive QC on these arrays, and I am
happy
with the quality of the data.
I have attached a plot of one of the dyeswap pairs. The left panel is
M
array 1 vs. M array 2. The highly correlated spots are indicated in
red. The right panel is A array 1 vs A array 2. The histogram is the
value of A for the highly correlated spots on array 1.
The correlation is even higher if I pair the wrong set of arrays
together
i.e. the correct blocking is 1,1,2,2 but if I put in 1,2,2,1 for the
blocks, 20% of the spots have correlation higher than 0.9.
If anyone has any ideas, I would be happy to hear them. The only
thing I
can think of is dye bias.
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111
