[BioC] Affymetrix data double normalisation
James W. MacDonald
jmacdon at uw.edu
Tue Sep 25 16:21:08 CEST 2012
On 9/25/2012 7:11 AM, Jun Han [guest] wrote:
> 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?
> Many thanks.
> -- output of sessionInfo():
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "indexProbes", for signature "ExpressionSet", "character"
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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