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library(GEOquery) | ||
library(limma) | ||
library(Biobase) | ||
library(dplyr) | ||
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data <- getGEO(GEO = "GSE58831", GSEMatrix = T, getGPL = T, AnnotGPL = T) | ||
assay <- data$GSE58831_series_matrix.txt.gz@assayData$exprs | ||
pheno <- data$GSE58831_series_matrix.txt.gz@phenoData@data | ||
feature <- data$GSE58831_series_matrix.txt.gz@featureData@data | ||
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#for exchanging prob ids into gene symbols of feature file of GEO | ||
#removing repetitive genes in data | ||
exdat <- assay[!duplicated(feature$`Gene symbol`[match(rownames(assay), rownames(feature))]),] | ||
#exchanging the unique rownames into gene symbols | ||
rownames(exdat) <- feature$`Gene symbol`[!duplicated(feature$`Gene symbol`)] | ||
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