Different from conventional method, however, the
limma method is proven effective in microarray analysis [35], even for a small sample size (2-5 cases) [36].
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).
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 [53].
In addition, relative array quality weights were computed via the
limma R-package [21] 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 [12].