[BioC] Limma and Dye-Swap/Single Channel

[Naomi Altman]

The problem with your method is not normalization but confounding.

Genotype differences and array effects cannot be distinguished in this design.

--Naomi Altman

At 11:23 AM 7/14/2004 +0200, S_Thieme wrote:
>Hello,
>
>I hybridized for two samples both Cy3-Label and Cy5-Label to one chip (i.e.
>wtCy3+wtCy5 and mutantCy3+mutantCy5.
>I would like to normalize that data, but how?
>I tried to use the array2channel funtion, but how do I use the result?
>
>My targets looking like this:
>    FileName Cy3 Cy5
>1 e85b.txt  WT  WT
>2 e87b.txt  WT  WT
>3 e88b.txt 139 139
>4 e89b.txt 139 139
>
>After array2channel:
>      Channel FileName Target
>1.1       1 e85b.txt     WT
>1.2       2 e85b.txt     WT
>2.1       1 e87b.txt     WT
>2.2       2 e87b.txt     WT
>3.1       1 e88b.txt    139
>3.2       2 e88b.txt    139
>4.1       1 e89b.txt    139
>4.2       2 e89b.txt    139
>
>Can I get a model.Matrix out of that? Or is it not possible to normalize
>that way of hybridization?
>
>Thanks!
>
>Sebastian
>
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>
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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