DiffExpAnalysis: Differentially expressed analysis

In miRLAB: Dry lab for exploring miRNA-mRNA relationships

Description

Find the top miRNAs and mRNAs that are differently expression between different conditions, e.g. cancer vs normal

Usage

DiffExpAnalysis(miR1, miR2, mR1, mR2, topkmiR, topkmR, p.miR, p.mR)

Arguments

miR1	the miRNA dataset for condition 1, e.g. cancer
miR2	the miRNA dataset for condition 1, e.g. normal
mR1	the mRNA dataset for condition 1, e.g. cancer
mR2	the mRNA dataset for condition 2, e.g. normal
topkmiR	the maximum number of miRNAs that we would like to extract, e.g. top 50 miRNAs.
topkmR	the maximum number of mRNAs that we would like to extract, e.g. top 2000 mRNAs.
p.miR	cutoff value for adjusted p-values when conducting differentially expressed analysis for miRNAs.
p.mR	cutoff value for adjusted p-values when conducting differentially expressed analysis for mRNAs.

Value

the dataset that includes differentially expressed miRNAs and mRNAs. columns are miRNAs and mRNAs and rows are samples

References

Smyth, G.K. (2005). Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor (pp. 397-420). Springer New York.

miRLAB documentation built on Nov. 8, 2020, 5:45 p.m.