[BioC] About package beadarray

[Anand Patel]

Hmm.  This and the image processing file from the current dev version
of the package (2.1.3) are seemingly inconsistent?
http://bioconductor.org/packages/2.8/bioc/vignettes/beadarray/inst/doc/ImageProcessing.pdf

Suggests that readIllumina always performs the backgroundNormalise process.

http://bioconductor.org/packages/2.8/bioc/vignettes/beadarray/inst/doc/beadlevel.pdf

and what's below suggests that this is not the case anymore.

Could you clarify?  My goal in asking is to take data that's been read with:

and use the neqc normalization process, which requires background
correction not have been applied.

Thanks,
Anand

On Tue, Dec 14, 2010 at 5:00 AM,  <bioconductor-request at r-project.org> wrote:
> Message: 3
> Date: Mon, 13 Dec 2010 14:24:45 +0000
> From: Mark Dunning <mark.dunning at gmail.com>
> To: Changhe Fu <fuchanghe at gmail.com>
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] About package beadarray
> Message-ID:
>        <AANLkTik5PWUwyhTBwWbqsoJcOCW9F68ED5uk8fEYfV=8 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> That function used to be in beadarray to implement the background
> normalisation that occurs in Illumina's BeadStudio/GenomeStudio.
> However, it has been shown in various studies to be inferior to other
> methods. See the neqc (limma) or vst (lumi) alternatives available
> through the normaliseIllumina function in beadarray.
>
> Mark
>
>
> On Fri, Dec 10, 2010 at 11:07 PM, Changhe Fu <fuchanghe at gmail.com> wrote:
>> Hi, All
>>
>> In previous version of package beadarray, I can use the function
>> backgroundNormalise(). But in new one, I cann't find it. Is it included in
>> some other fuction of normalising?
>>
>> Thank you
>>
>> --
>> Best,
>> Changhe Fu
>>
>> ? ? ? ?[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>