[BioC] Illumina Beadarray negative data

[Sean Davis]

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