Tim,

Thanks for your answer!!

Hajar

2010/11/12 Tim Triche <tim.triche@gmail.com>

> yes -- the text files have local bgcorrection applied.
>
> truncate the intensities at a minimum of 0 or 1 if the
> negative-photons-bouncing-off-the-array business bothers you (what with it
> being at odds with the way the universe works and all).  This also avoids
> later irritations from other libraries.
>
>
>
> On Fri, Nov 12, 2010 at 1:35 PM, Hajar Hassani Lahsinoui <
> hajar.hassani@gmail.com> wrote:
>
>> Hi everyone,
>>
>> I tried to read beadarry data in R with backgroundMethod="none". For some
>> reason it still gives me the array's with a background correction. See
>> below. Does this mean my "raw data" has allready been background corrected?
>> I couldn't find it in the report.
>>
>> Thanks,
>>
>> Hajar
>>
>>
>> BLData=readIllumina(arrayNames=array.namen,backgroundMethod="none",normalizeMethod="Quantile",useImages=F)
>> 'useImages=FALSE': please check that the 'singleChannel'
>>            argument is appropriate for your data set
>> Found 24 arrays
>> Reading raw data from ./5513091009_A_perBeadFile.txt
>> Reading locally background corrected intensities
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>>
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>
>
>
> --
> If people do not believe that mathematics is simple, it is only because
> they do not realize how complicated life is.
> John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>
>
>

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