[BioC] limma: positive correlation for dyeswap pairs

Naomi Altman naomi at stat.psu.edu
Sat Aug 6 02:57:17 CEST 2005

The cause of the positive correlation among the dye-swap technical 
replicates appears to be a huge amount of dye bias, which appears to have 
been due to a poor labeling reaction in one channel.

A dye-swap pair with similar plant material and a fresh labeling kit did 
not exhibit this dye bias.


At 04:51 PM 8/3/2005, Naomi Altman wrote:
>My plots were not attached to the previous message.
>The plots shows one of the 2 biological replicates.  The dye-swap 
>technical replicates are plotted against one another.  13% of the genes 
>have correlation greater than 0.9, as computed by duplicateCorrelation.
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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

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