[BioC] Normalisation of Agilent microRNA arrays using inbuilt controls?

[Wei Shi]

Dear Daniel:

    You might need to check the quality of these negative controls to 
see if they provide a good measurement of the background noise. One way 
to do this is to use the density function to check if these probes are 
normally distributed.

    If the negative control probes are a good representation of the 
background noise, you can consider using these controls to estimate the 
background mean intensity and the standard deviation of the background 
intensities which are two of the parameters needed by the normexp 
background correction model. The limma function neqc uses the negative 
controls and positive controls to do the normalization which might be 
useful for your data.

Cheers,
Wei

Daniel Brewer wrote:
> Hello,
>
> I have been trying to work out the best way to normalise microRNA
> microarrays recently as there seems to be some debate about whether the
> normal mRNA assumptions hold.
>
> The AgiMicroRna suggests using quantile or scale, whereas other posts I
> have read have suggested VSN.
>
> My question is whether the control probes on the Agilent chip could be
> used o do the normalisation i.e. the Negative and Positive Control probes.
>
> Would this be a good idea?  And how would one go about this? A loess
> using the weights to define what probes are used?
>
> Thanks
>
> Dan
>
>   

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