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

From: Peter Wilkinson <pwilkinson_at_videotron.ca>
Date: Thu 29 Jul 2004 - 13:33:25 EST


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



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https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jul 29 13:41:43 2004

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