[BioC] Illumina Beadarray negative data

[Wei Shi]

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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>>
>>