[BioC] dye-swap and arrayMagic

[michael watson (IAH-C)]

The dye-swap columns need to be multiplied by -1 if they are log ratios

-----Original Message-----
From: Dr_Gyorffy_Balazs [mailto:zsalab2 at yahoo.com] 
Sent: 06 July 2004 10:35
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] dye-swap and arrayMagic


Hallo everyone!

I have analysed 108 Genepix arrays using the arrayMagic package. However, I have a problem: every second array is a repetition of the previous array with dye-swap (normal: 1, 3, 5, ... dye-swap: 2, 4, 6, ...). How can I correct the logratios output (the writeToFile function) in order to get the correct values for the dye-swapped chips?

Thank
Balazs Györffy

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