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Moreover, it has been shown that using only a single control gene can lead to appreciable normalization errors and that using several normalizers is preferable in order to compensate for the potential biases introduced by an inappropriate normalizer [19], [21] [22].
In order to minimize false discovery due to normalization errors, we cross-validated the data by two complementary approaches.
The short integration time of 26.2 ms introduces normalization errors and distortions at large τ for such slowly decaying autocorrelation functions, making meaningful determination of 〈Δ φ〉 difficult.
Note, however, that in general, small gene expression changes have more uncertainty and are more sensitive to normalization errors than large expression changes.
Identification of candidate genes useful for normalization has become a major task, as it has been shown that normalization errors are probably the most common mistake, resulting in significant artefacts that can lead to erroneous conclusions [ 2].
An arbitrary threshold was utilized for two reasons: first, to account for normalization errors, and second, to account for the fact that replicate data did not result from repeated hybridizations with the same RNAs but from repeated probe spotting.
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This approach is not affected by the inter-sample noise due to normalization error and captures information about whether COX-2 is both a highly expressed gene within the transcriptome of a given sample.
In order to estimate the proportion of normal cells in a mixed sample, it is necessary to also adjust the LRR baseline if there is a genome-wide LRR value shift (an upstream normalization error leading to LRR value zero not mapping to copy number 2).
Rankings based on comparison alone are insensitive to those correlations, and the normalization of errors makes aggregation possible without going through the complex exercise of modeling the relations between settings.
It includes tables of the model equations, further supporting experimental results and explanations for data normalization and error calculus.
Data processing, normalization, and error modeling were performed using the Rosetta Resolver system (version 7.2; https://www.rosettacommons.org/software).org/software
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