[BioC] liimma and Across Array Normalisation

[Saket Choudhary]

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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