limma powers differential expression analyses for RNA-sequencing and microarray studies
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Cites methods from "limma powers differential expressio..."
...Specifically, the objects are summarized in a ‘SummarizedExperiment’ object (3) to allow easy integration with other Bioconductor packages, such as GRanges (25), IRanges (25), limma (26) and edgeR (27)....
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Cites background from "limma powers differential expressio..."
...…Ingenuity Pathway Analysis QIAGEN http://www.ingenuity.com/products/ipa R The R Foundation https://www.r-project.org/ R - Limma package Ritchie et al., 2015 https://bioconductor.org/packages/ release/bioc/html/limma.html R - Plyr package Wickham, 2011…...
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References
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"limma powers differential expressio..." refers background in this paper
...Users can control either the family-wise type I error rate or the false discovery rate (46)....
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...Such a plot is called a Bland-Altman plot [36] or a Tukey mean-difference plot [10]....
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