[BioC] dealing with negative values in illumina

Wolfgang Huber whuber at embl.de
Sat Jun 11 23:14:47 CEST 2011

Hi Matt

you could try the function 'vsn2' (package: vsn), it is designed to find 
that type of additive offset automatically (the mathematical details are 
a bit more complex but that's the gist of it). Let me know if the 
vignette or the accompanying paper are unclear.

	Best wishes

Il Jun/8/11 6:44 PM, Arno, Matthew ha scritto:
> Simon - just read your message on negative illumina data. I'm faced with the same thing and it is definitely fluorescent intensities with negative values. It ranges from approx. -200 to +20,000. I'm thinking that it's maybe background subtracted and that's where the negative values are coming from. If that's the case could we add a constant to all the data (equal to ~200) to bring it up to minimum of 0.0 or thereabouts?
> Matt
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Wolfgang Huber

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