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Genes differentially expressed between chimpanzee and human testis, and genes that are differentially expressed at different stages of mouse spermatogenesis, were identified using Limma (linear models for microarray data) implemented in R software [74].
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We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system.
Data were analyzed using Linear Models for Microarray Data (LIMMA) implemented in R [ 41].
Normalization and analysis of the microarray data were implemented using Bioconductor.
We designed a key-value [ 18] based data model to support faster queries over large-scale microarray data, and implemented the schema using HBase.
Microarray data analyses were implemented with the limma package (MEV platform, v4.9.0) [ 29, 30].
The microarray data processing method implemented in the PlantRGS for the identification of most suitable reference genes is based on the previous studies.
This software was initially developed for microarray data analysis and implements a modified t-test useful to verify large number of independent hypothesis.
Significance Analysis of Microarrays (SAM) is a non-parametric statistical test based on a permutation approach specifically implemented for microarray data [61].
Affymetrix microarray data were analyzed using methods implemented in the R/Bioconductor platform.
Differential expression analysis was done using the Linear Models for Microarray Data (limma) method [ 10] implemented in the limma package in R.
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