[BioC] Illumina Beadarray negative data

[Wei Shi]

You will get negative expression values if your data are global background
corrected. Our microarray facility core creates two types of datasets: (1)
Not background corrected and normalized and (2) background corrected and
normalized. Background values can be seen in the probe control profile
output from BeadStudio.

Wei

> On Nov 9, 2007 11:02 AM, affy snp <affysnp at gmail.com> wrote:
>> Hi Sean,
>>
>> Thanks a lot for the suggestion. I checked with our microarray
>> facility folks and they told me that they did background
>> subtraction and then normalized the data in BeadStudio.
>> Should we also skip the background subtraction step?
>
> The negative values are generated by the normalization step, I
> believe.  So, you can do background subtraction or not.  The choice to
> opt out of background correction is relatively new in BeadStudio, I
> think, so I do not have a systematic answer as to whether or not it is
> warranted to use BeadStudio background subtraction or not.  Perhaps
> others will have strong opinions one way or the other.
>
> Sean
>
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