[R] Re: [BioC] normalisation for universal reference in 2 channel arrays

[Peter Wilkinson]

Thanks for the suggestions,


one option i was thinking was to center the universal channel and sample 
channels by normalising the medians of each column of the matrix on each 
channel. But I don't know if it is appropriate to do a loess after this?

Does the quantile option actually do this?

Peter

At 06:59 PM 7/28/2004, you wrote:
>At 06:02 AM 29/07/2004, Peter Wilkinson wrote:
>>I would like to know some alternative to normalization for 2 channel 
>>experiments against universal, where samples may have been hybridized in 
>>seperate batches where the universal RNA has changed lot (should not have 
>>happened but it did). What is the same between the batches is that what 
>>looks like up-regulated compared to the universal iis upr-egulated, and 
>>what is down-regulated looks down-regulated. The difference is that the 
>>down-regulated (and not in the up), so so much more down-regulated in one 
>>of the batches. It looks like to be that the universal has more mRNA 
>>abundance in one batch over the other.
>
>Gquantile won't help because it doesn't change the M-values. (It is 
>intended for use with single channel analyses.) You could try 'quantile' 
>or 'scale' normalization (not both) but there are no magic bullets in a 
>situation like this. If you use 'scale normalization, you should always do 
>within-array normalization first. If you use 'quantile' normalization, the 
>within-array normalization step is optional.
>
>Gordon
>
>>so ...
>>
>>I have samples that can be divided into 2 classes: 0,1, and within each 
>>class I have samples that have been run at different times. I would like 
>>to treat my universal channel uniformly across all samples (assuming that 
>>my universal changed lot), and then adjust the Sample (Red) channel to that.
>>
>>is the normalizeBetweenArrays with the method="Gquantile" option the 
>>right option for this?
>>
>>What is the complete work-flow for this case? And after I have normalized 
>>within the Arrays, can I go on to scale option for normalizing between arrays.
>>
>>Peter