I have looked at the spots causing this, and I do not see evidence of dye bias on the scale necessary to cause this. --Naomi >To: bioconductor at stat.math.ethz.ch >From: Naomi Altman <naomi at="" stat.psu.edu=""> >Subject: limma: positive correlation for dyeswap pairs >Cc: >Bcc: >X-Eudora-Signature: <work> >Date: Tue, 02 Aug 2005 16:48:16 -0400 > >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 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