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Statistical Analysis

SB Shayantan Banerjee
AM Akram Mohammed
HW Hector R. Wong
NP Nades Palaniyar
RK Rishikesan Kamaleswaran
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Affymetrix data download and gene mapping were done using the “affy” and the annotation package “hgu133plus2.db” package in R, respectively. A Fisher exact test was performed to determine the statistical significance among the functional enrichment terms. Benjamini Hochberg's multiple test correction methods were used to calculate the differentially expressed genes (DEGs). Heatmap for the DEGs was generated using the Heatmap () from the “complexHeatmap” package (33) in R. Since there was no explicit argument in the Heatmap () to scale the rows/columns, we scaled our expression matrix using the scale () (28) and then constructed the heatmap of the resulting scaled matrix. The Volcano plot and the MA plot were generated using the volcanoplot () and plotMA () of the limma package (29), respectively.

Copyright and License information:  ©2021 Banerjee, Mohammed, Wong, Palaniyar and Kamaleswaran.
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