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Different from conventional method, however, the limma method is proven effective in microarray analysis , even for a small sample size (2-5 cases) .
A linear model for differential expressions was applied to the resulting submatrices using the moderated t statistics implemented in the limma package (Ritchie et al., 2015).
Of these 827 ions, we retained only those with significantly changing intensities, either over time or across different treatments compared to the control treatment, using the limma method .
Moreover, edgeR and limma were used to obtain candidate DEGs, respectively, and get intersection set.
After the data were preprocessed and normalized, limma package in R was applied to identify the differentially expressed miRNAs.
Le coup d'envoi de la 13e edition de ce festival, dedie cette annee a la Palestine et au regrette Aziz Djemame, disparu il y a deja 10 ans, membre fondateur de l'association Limma qui a donne naissance au Dimajazz, avait ete donne le 27 novembre dernier.
Differentially expressed miRNAs were obtained by applying linear models with R limma package (Gordon Smyth; Bioconductor project, http://www.bioconductor.org), implemented in the POMELOII tool (http://asterias.bioinfo.cnio.es/).
Spots with a signal-to-noise ratio > 0 or control probes were selected and normalized by the R program of the limma package (Smyth and Speed 2003).
The user can then proceed with his usual analysis pipeline, for example, "rma"and "limma" The package also contains some utility functions for generating assessment figures similar to those found in this paper; users are referred to the package's internal documentation for instructions.
For each CpG site, differential methylation between specimens collected from women with FM and controls was tested using the moderated t-test in the limma Bioconductor package [51, 52] in the R programming environment .
In addition, relative array quality weights were computed via the limma R-package  using the algorithm by Ritchie et al.
The differential expression analysis was performed using limma package in Bioconductor, and the false discovery rate (FDR) was controlled by adjusting P values based on the Benjamini and Hochberg multiple testing procedure .
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