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Microarray data were preprocessed (background subtraction, normalization, and summarization) using robust multi-chip analysis (RMA) [18].
Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform.
Rather, once data gathering and data analysis applications become semantically interoperable, at the very least, those who acquire the illustrative microarray data should expect their own machines to automatically trigger its sensible analysis by background subtraction, normalization and basic multivariate exploratory analysis such as dimensionality reduction and clustering.
Spot detection was performed using default setting for detection, background subtraction, normalization and matching.
After background subtraction, normalization and filtering the raw intensity values were used for analysis.
All expression levels were analyzed using background subtraction, normalization and summarizing probe sets.
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Printing, staining, scanning, background subtraction, normalization relative to β-actin signal, and data analyses were performed as described previously [34].
This often includes image analysis, filtering of data and background subtraction before normalization and transformation of data.
GeneSpring (ver. 10) software (Agilent Technologies) was used for background subtraction, LOWESS normalization, and extraction of normalized raw signal intensities for all probe sets from each array.
Offset background subtraction, loess normalization and least square regression were used along with moderated t-test and empirical Bayes statistics.
TiArA aims to be an integrative platform upon which the user can perform the background subtraction, data normalization, and generate a summary report all in one application for any Affymetrix chip including customized designs.
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