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Figure 3 | Genome Biology

Figure 3

From: Towards the uniform distribution of null P values on Affymetrix microarrays

Figure 3

Estimates of standard error do not survive quantile-quantile normalization. (a,b) x ¯ 1 x ¯ 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2Caerbhv2BYDwAHbqedmvETj2BSbqee0evGueE0jxyaibaiKI8=vI8tuQ8FMI8Gi=hEeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciGacaGaaeqabaqadeqadaaakeaaieaaceWF4bGbaebadaWgaaWcbaGaaGymaaqabaGccqGHsislceWF4bGbaebadaWgaaWcbaGaaGOmaaqabaaaaa@381E@ (panel a) and σ2 (panel b) before and after background correction and quantile-quantile normalization for the comparison of the Latin Square experiments 1 and 2. Fits shown are to a linear regression. (c) Box plot showing the R2 values from a linear fit for all 14 2× Latin Square comparisons.

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