[BioC] About package beadarray

[Anand Patel]

That does clear things up.  I actually determined that this was the
case by looking at the columns in the BeadLevel data (no Grn.bc), but
found the docs confusing.

Incidentally, after kludging the C source files of the beadarray
package to force the parallel code, it's spectacularly fast at reading
the data (for some reason, the -fopenmp flag in gcc 4.2.1 on OS X
doesn't properly respond to ifdefined _OPENMP, so I removed the ifdefs
altogether and used the multithreaded code lines directly).  Not sure
why it wouldn't compile multithreaded in the first place, but someone
more familiar with the OS X compiler system could probably get it to
work.  It's nice to use the Mac Pro's cores.

Thanks,
Anand

On Mon, Jan 10, 2011 at 5:34 AM, Mark Dunning <mark.dunning at gmail.com> wrote:
> Hi Anand,
>
> I think I understand the source of your confusion. There are two types
> of correction applied to BeadArray data; one at the bead-level and one
> at the summarized level.
>
> The bead-level text files created by Illumina's scanning software
> report the intensity of each bead on the array. These have been
> adjusted by subtracting a local background measure calculated using
> nearby pixels on the image. For convenience, the readIllumina function
> in beadarray will read these values, as these are the same values that
> are analysed by Illumina's BeadStudio/GenomeStudio software. We find
> them adequate for most purposes, although a more thorough analysis is
> possible as described in the imageProcessing vignette. If you have
> data exported from BeadStudio they will almost certainly have been
> adjusted in this way.
>
> However, the backgroundNormalise method (that is now removed) referred
> to in previous emails occurs on a per bead-type basis once data have
> been summarized. It used to be the default normalization method in
> BeadStudio. The quantities subtracted are negative controls
> (bead-types with no target in the genome). As I mention in previous
> posts there are viable alternatives to this method. The neqc method
> you are interested in requires summarized data and (I suspect)
> developed with GenomeStudio data in mind. Therefore it is Ok to use
> data that have been read using readIllumina with this method.
>
> Hope this helps. Regards,
>
> Mark
>
> On Thu, Jan 6, 2011 at 8:37 PM, Anand Patel <acpatel at gmail.com> wrote:
>> 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]]
>>>>
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>>
>