In amcdavid/PenultimateGEXContainer: Penultimate gene expression container: An interface for interchange of gene expression data

Habib 2016 data

library(Biobase)
library(ArrayExpress)
library(GEOquery)
library(SummarizedExperiment)
habib_ae = getAE('GSE85721')
sdrf <- Biobase::read.AnnotatedDataFrame(habib_ae$sdrf, habib_ae$path,  blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote = "\"")
expdat = ArrayExpress:::readExperimentData(habib_ae$idf, habib_ae$path)

geo <- getGEO('GSE85721')
se <- makeSummarizedExperimentFromExpressionSet(geo[[1]])

We'd need to parse some of the array express data to get a link back to the protocols and SRA #

amcdavid/PenultimateGEXContainer documentation built on May 12, 2019, 2:35 a.m.