Sentence examples for array effect in from inspiring English sources
We fit an analysis of variance model to each probe fitting expression as a function of RNA quality with four approximately equal-sized categorical levels in the mother-newborn study (RIN<5.3; 5.3
For 5.5% of the genes, the inclusion of an array effect in the linear model resulted in lower BIC values (Table 1).
In particular, when the quality of the spot printing procedure is not constant (often the case with in-house spotted arrays), it is essential to account for an array effect in the ANOVA model [ 9].
The observation that ratio-derived p-values can be improved by intensity-based models can be attributed to the inclusion of the array effect in the ratio-based linear model.
Accounting for such an array effect in the analysis of dual-color arrays was initially necessary due to the relatively poor quality of array platforms: researchers were confronted with different levels of background signals across arrays, and the process of spotting cDNAs yielded probes with different shapes and probe concentrations.
In the first scenario, we demonstrate how to estimate array effects in the presence of biological signal.
Normalization methods potentially mitigate effects more properly considered as batch effects or array effects in addition to addressing the adjustment discussed in this paper.
For dual-color arrays specifically, an array effect is included in the model to determine the technical noise introduced by any between-array differences.
When intensities instead of ratios were taken into the statistical analysis, no differential genes were detected at a FDR of 10% unless dye and array effect were included in the model.
However, we conclude from our experiments that for both the brain and cell line datasets, the array effect is too small in comparison to the main factor of interest (treatment) to justify incorporation into the ANOVA model.
It should be noted that we do not state that the array effect is absent: our analyses in fact show that an array effect is present in modern dual color microarray experiment.
