[BioC] Illumina Beadarray negative data

[affy snp]

Dear Wei,

Thanks a lot for the notes. We have also figured out by the help
of Illumina experts that the negative expression values were generated
by background subtraction.

Our facility used the BeadStudio to do background subtraction and
normalization steps. The only concern I have is that we often see,
for a probset, it perhaps has positive value for control sample while
negative value for the test sample, or the opposite. For this scenario,
I do not know how to deal with.

Have you also done the analysis starting with the dataset1 you mentioned?
Will that make a difference?

We will also obtain the raw dataset without background subtraction and
see how it will look like.

Thanks once again!

Allen

On Nov 11, 2007 7:13 AM, Wei Shi <shi at wehi.edu.au> wrote:
> 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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