full_data: Gene expression matrix

In GSSTDA: Progression Analysis of Disease with Survival using Topological Data Analysis

Gene expression matrix

Description

Matrix containing gene expression profiling of 104 breast cancer and 17 normal breast biopsies. Expression profiling data by array (platform HG-U133_Plus_2).

Usage

data(full_data, package = "GSSTDA")

Format

Gene expression matrix with 4165 rows and 121 columns.

The columns correspond to the patients and the rows to the genes. The column names correspond to the patient identifier in GEO. The row names correspond to the gene names.

Details

Normalized gene expression data GSE42568. Background correction, summarization, and quantile normalization were carried out using the fRMA method implemented in the fRMA package. Filtered probes that did not target genes with valid gene id were filtered and those probes targeting the same gene were collapse by thanking those presenting the highest row variance using the WGCNA::collapseRows function. Subsequently, due to CRAN publication requirements, the number of genes is randomly reduced to 4165 genes.

Source

The data are from the study GSE42568 available in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568. The data were processed as explained in the details section.

GSSTDA documentation built on June 22, 2024, 10:44 a.m.