[BioC] liimma and Across Array Normalisation

[Saket Choudhary]

Hello Gordon,

I had a chance to go through the paper. I have a set of negative and
positive controls, arising out of single channel Genepix platform.
>From what I could gather, 'nec' method in limma performs
backgroundcorrection using these negative control spots.

However one of the inputs to 'nec' is also "detection.p", which the
.gprs don't have.

I could simply take a mean of all the negative controls E and Eb, and
subtract it from each probe's E&Eb, doing it for all the arrays. Would
this mimic what I want to acheive with the 'nec' function?

Saket

On 6 February 2014 13:04, Saket Choudhary <saketkc at gmail.com> wrote:
> Hello Gordon,
>
> Unfortunately I do not have access to this as of now. I will however
> get hold of it soon.
>
> After implementing this, I would expect the 'CONTROL' to have similar,
> if not same values, right?
>
> However some of the values for these Control genes after the
> normalisebetweenarray step have high variance. Is this behaviour
> normal or am I missing something?
>
> Saket
>
> On 6 February 2014 06:32, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>> If 'x' is your background-corrected EList, then
>>
>>   w <- rep(1,nrow(x))
>>   w[controls] <- 100
>>   y <- normalizeBetweenArrays(x, method="cyclicloess", weights=w)
>>
>> does what you want.
>>
>> For an example of this approach:
>>
>>   http://rnajournal.cshlp.org/content/19/7/876
>>
>> Best wishes
>> Gordon
>>
>> --------- original message ----------
>> Saket Choudhary saketkc at gmail.com
>> Thu Feb 6 06:59:42 CET 2014
>>
>> I am analysing a proteomics microarray data set for a two group
>> sample(Normal and Disease) using single color channel. The arrays have a set
>> of pre-defined CONTROL points whose expression levels are supposed to be
>> similar/same across all the arrays.
>>
>> I would like to 'normalise' the levels of all probes such that normalisation
>> ends up with all CONTROL points having similar expression levels. If I
>> understand it right, normalizebetweenarray does not allow this kind of
>> normalisation.
>>
>> Is there a pre-implemented function to do this? If not, what would be a way
>> to acheive this kind of normalisation?
>>
>> Code: https://gist.github.com/saketkc/8669586
>>
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