[BioC] Illumina Beadarray negative data

[affy snp]

Thanks Wei. Fairly enough. I guess I will run to our microarray facility
tomorrow to request the slides re-scanned. BTW, I guess you are using
Lumi or Beadarray for normalization step?

Regards,
      Allen

On Nov 11, 2007 5:28 PM, Wei Shi <shi at wehi.edu.au> wrote:
> Dear Allen:
>
>     We always work on the data set which are not background corrected
> and normalized. There are no negative expression values in this data set.
>
> Cheers,
> Wei
>
>
> affy snp wrote:
> > 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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> >>
> >>
>