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NRI conceived and coordinated the study, carried out the statistical analysis of the normalization, co-wrote the manuscript.
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In addition, an aliquot of cell lysates was subjected to western blot analysis for the normalization of each transfection efficiency.
A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed.
Structural MRI analysis relies on the normalization of the natural variations in brain size and shape to fit a predefined spatial template and allow standardized comparisons to be made at a group level.
We focus on the analysis of between-array normalization steps, i.e. we assume the data to be analyzed has already passed a primary normalization covering for variances due to localization of the probe sequences on the array, GC-content of the probe sequences, varying sensitivity in different detection ranges, and others.
The raw files were stored in genepix files compatible with the LIMMA library of the R-project statistical and Bioconductor environment [ 46] which was used for the normalization and analysis of the data.
The detailed analysis of the leaf libraries revealed that the normalization leads to increased coverage since a larger number of AGIs is identified by 5 and 10 reads, respectively.
In the analysis of aCGH data, normalization is deemed a critical pre-processing step.
During our analysis we recognized the strong influence of the normalization scheme on the performance of the distance measures.
TH completed the normalization and SAM analysis of the chips data and participated in the writing of the manuscript.
Normalization and analysis of the microarray data were implemented using Bioconductor.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com