Hi Maria,

The RANDOM probes on the NimbleGen arrays are randomly generated probes
with the same length and GC content characteristics as the experimental
probes on the array. They are meant to give researchers an estimate of the
signal from non-specific binding on the array. There should be no harm in
carrying them through the analysis, and the final expression value
generated for those probes can be a useful threshold for estimating which
transcripts are expressed above the background level.

Todd


On Thu, Jan 10, 2013 at 6:24 AM, María José Rivas <marivas@uvigo.es> 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???
>
> Thanks in advance,
>
>
> --
>
> María José Rivas Quelle (PhD. Student)
> Área de Genética (Grupo Xb2)
> Dpto. Bioquímica, Genética e Inmunología
> Facultad de Biología 36310
> Universidad de Vigo (SPAIN)
>
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>
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-- 
Dr Todd Richmond, PhD
richmond.todd@gmail.com

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