[BioC] Affymetrix data double normalisation

[James W. MacDonald]

Hi Jun,

On 9/25/2012 7:11 AM, Jun Han [guest] wrote:
> Hi,
> I would like to use gcrma to do a within group normalization first (30 groups in total), then input all the normalised 30 groups to do another global gcrma.
> Is this possible? Does the gcrma accept the inputs from the first normalisation output?

The short answer is no. When you run gcrma(), you do background 
correction, normalization, and finally summarization of the probe-level 
data, resulting in probeset-level data. In other words, you are taking 
the PM probes and summarizing them into a single value at the probeset 
level (after background correcting and normalizing).

Since gcrma() expects you to be inputting an AffyBatch containing PM and 
MM probe data, it fails when you input an ExpressionSet containing 
summarized probeset level data.

I assume you are trying to combine two groups that you think should not 
be normalized and summarized together. This leads to two questions - 
first, why don't you think these data can be combined prior to the 
gcrma() step, and second, if the answer to the first question is because 
of a batch effect, have you looked at e.g., sva or comBat?

Best,

Jim


> Many thanks.
> Jun
>
>   -- output of sessionInfo():
>
>> gcrma12<-gcrma(gcrma1,gcrma2)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "indexProbes", for signature "ExpressionSet", "character"
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099