[BioC] Illumina Beadarray negative data

[Wei Shi]

Yes, we are using Lumi VST to do the data transformation at this stage.

Good luck,

Wei

affy snp wrote:
> 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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>>>>>
>>>>>           
>>>>