miRExp: miRNA expression data

Description Format Details

Description

miRNA expression data

Format

miRExp: A SummarizedExperiment object with 72 BRCA and 72 normal samples (rows) and 226 miRNAs (columns).

Details

The matched breast invasive carcinoma (BRCA) miRNA, lncRNA and mRNA expression data is obtained from TCGA (http://cancergenome.nih.gov/). The data focuses on 72 individuals for which the complete sets of tumor and matched normal (i.e., normal tissue taken from the same patient) profiles are available. A miRNA which has missing values in more than 10 are imputed using the k-nearest neighbours (KNN) algorithm from the impute R package. We use the limma R package to infer differentially expressed miRNAs, ceRNAs and mRNAs between tumour and normal samples. After the analysis, we select top 226 miRNAs which are differentially expressed at a significant level (adjusted p-value < 1E-02, adjusted by Benjamini & Hochberg method).


zhangjunpeng411/miRSM documentation built on Nov. 28, 2020, 7 a.m.