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Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios.
The dataset normalization called also feature scaling is a mandatory preprocessing step before staring the classification task.
Currently, several methods are available for dataset normalization.
A Principal Component Analysis (PCA) and Heatmap were used to confirm dataset normalization.
In the total gene dataset, normalization is done on all genes.
KATS carried out the Affymetrix gene expression dataset normalization and contributed to the manuscript draft (Materials and methods section).
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The proposed mechanism of selecting appropriate houskeeping genes for inter-dataset normalization is robust and accurate for differential expression analyses.
Although this cross-dataset normalization approach is not ideal, it can still retain most of the pattern in the data, leading to valuable findings regarding gene function similarity.
Figure 9: In the Platinum Spike dataset, all normalization methods resulted in similar detection of differential gene expression, with MedianCD and SVCD normalization being only marginally better.
Although this could skew the observed raw citation counts toward disciplines that are better represented within the dataset, the normalization by discipline mitigates such biases.
This sample was excluded from the dataset before normalization.
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