[BioC] arrayQualityMetrics: expression or probe-level data?

[Wolfgang Huber]

Dear Efthimios

On 12/2/11 5:29 AM, Efthimios MOTAKIS wrote:
> Hello all,
>
> I have a question regarding "arrayQualityMetrics" and I could not find
> relevant information at the posted Q/A.
>
> I have a dataset of 80 U133A Affymetrix .cel files coming from an
> ovarian cancer study (patients' samples). When I run
> "arrayQualityMetrics" to the background corrected (RMA) and normalized
> (quantiles) probe-level data (thus processing the non-summarized
> AffyBatch object) I get a PCA showing two distinct groups (not a random
> separation; the first 40 cells belong to one group and the other 40 to
> the other). I also get 2 outliers (based on 5 out of the 6 different
> plots provided).
>
> When I run "arrayQualityMetrics" to the RMA or gcRMA expression data the
> two groups effects on PCA and the outliers disappear completely.
>
> Can summarization have such a strong influence to my data?

Are your non-summarized logarithm transformed? If not, then it is 
plausible that the PCA is driven by the behaviour of a few genes with 
large values, and that that effect goes away when you logarithm transform.

> Should I rely
> on the .cel files or the expression results for my analysis

Rely on whatever you use subsequently for your biological analysis, thus 
presumably the expression values.

	Best wishes
	Wolfgang

>
> Thank you,
> Makis
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber