Re: [base] procedure for obtaining normalized data

[<ja...@th...>]

Hi,

I think this is a problem with negative and zero intensity values (due 
to FG-BG). You need to decide how to treat these intensities and the 
filter or modify these numbers. After resolving this, you can proceed as 
you describe.


Cheers,

Jari


Ana Conesa wrote:
> Hi
> 
> I am using BASE to store and analyze 2 color (GenePix) data from a
> costum cDNA array.
> I am addressing now the analysis of an experiment. I created a raw bioassay
> out of raw data files and I would like now to normalize. I am not sure
> which is the standard procedure to do this. At first I calculated FG-BG
> using the formula intensity calculator and then I tried to compute M
> values on the result as log2(ch1/ch2) with the idea of running lowess
> normalization on this result, but this is giving me a "value" error, so
> I guess this is not the way. Could anyone give me a bit of help on this
> Thanks a lot
> Ana
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
> 

-- 
Jari Hakkinen, PhD
Complex Systems Division                        mailto:ja...@th...
Department of Theoretical Physics               phone: +46 (0)46 2229347
Lund University                                 fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden          http://www.thep.lu.se