[BioC] Fwd: limma: positive correlation for dyeswap pairs

[Naomi Altman]

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:
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>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