[BioC] Feedback on Affymetrix background adjustment

[James W. MacDonald]

Hi Anjan,

On 9/28/2010 5:03 PM, ANJAN PURKAYASTHA wrote:
> Hi,
> I have a data set of 3 biological repeats.
> My proposed workflow for data pre-processing: background adjustment ->
> normalization( lowess normalization to a median array)->  Li and Wong's
> method of model-based calculation of expression index.
> Any thoughts on which method of background adjustment to use (RMA; MAS;
> Ideal mismatch) would be highly appreciated.

I'm not sure what you mean by '3 biological repeats'. Three per group? 
Three total samples? How many samples total do you have?

Assuming you have few chips (3 or 6 or so), Li and Wong isn't going to 
work too well for you. If you look at the help page for this function 
you will see that the recommendation is to have at least 10 arrays.

If you are sure you like Li and Wong's algorithm, you will likely be 
better served by using dChip.

Best,

Jim


> Thank you in advance.
> Anjan
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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