[BioC] Nimblegen arrays; random probes

[James W. MacDonald]

Hi Maria,

On 1/10/2013 9:24 AM, María José Rivas wrote:
> Hi all,
>
> I have an experiment with 72 cDNA Nimblegen arrays. I notice that the
> arrays have some probes type RANDOM (I guess that there are control
> probes). I have performed the normalization doing:
>
> 1. Background correction
>
> RG50_bg<- backgroundCorrect (RGback, method="normexp", offset=50)
>
> RGback$printer<- list(ngrid.r=1, ngrid.c=1, nspot.r=nrow(RGback),
> nspot.c=ncol(RGback))
>
>
> 2. Between-array normalization
>
> MA.q_50_bg<- normalizeBetweenArrays(RG50_bg, method="quantile")
>
> In the object MA.q_50_bg there are still random probes. Should the
> normalization removes them??? Or is normal doing the analysis with random
> probes???

The normalization simply attempts to adjust the array distributions in 
order to account for technical variability. There is no removal of 
probes (and how would a function designed to work on arbitrary arrays 
know which probes to remove?).

If these probes are in fact controls (which you don't seem to know, and 
as the analyst it is your job to know these things), then you can argue 
that they should be removed at some point. The usual prescription is to 
remove after the eBayes() step.

Best,

Jim


>
> Thanks in advance,
>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099