[BioC] limma: positive correlation for dyeswap pairs
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)
>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)
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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