As the quantitation of serum HHV-6 IgG is based on normalization to total serum IgG, it became evident that natalizumab-treated MS patients had lower levels of total serum IgG than non-natalizumab treated MS patients from the same center (Figure 3C).
All results described below are based on RMA normalization of data from each center separately.
Raw reads were normalized using DESeq to adjust for differences in library sizes; figures displaying quantified RNA expression levels are based on this normalization.
In our program, we employed three normalization methods including linear normalization, nonparametric empirical Bayes correction normalization and quantile normalization, which are based on different assumptions of the data distribution.
Three optional normalization methods are provided in QChIPat, including linear normalization, nonparametric empirical Bayes correction normalization and Quantile normalization, which are based on different assumptions of the data distribution.
The findings in this study are based on an intuitive and efficient normalization method for comparative analysis.
The key principles underlying the design of traditional relational databases are based on the theory of database normalization, which dictates how the schemas in a database should be organized to minimize duplicate information across multiple tables, to reduce wasted storage of null values, and to ensure that the dependencies among data items are correctly manifested in the database.
Most normalization strategies are based on the reaction kinetics of re-association of denatured DNA.
The latter normalization methods are based on either linear scaling or sample quantiles instead of modeling sequence count data.
We normalized the 450K array data using Functional Normalization (FunNorm), a novel between-array normalization method, which is based on quantile normalization and uses control probes to act as surrogates for unwanted variation [ 19, 20].
