In AweKevin/DealGPL96: Dealing GPL96 RAW.tar file

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

GEO provides a wealth of biology related data, and GPL96 (Affymetrix Human Genome U133A Array) is one of the the most common biological chip platform. Although the post-processed matrix data are always provided, but the data produced from RAW data are most convincing! Here we developed to deal GPL96 RAW.tar file using the robust multi-array average expression measure, and returns data frame which is expression profile. Plus: DealGPL96 function can filter cels which are not of GPL96 platform in the RAW.tar file.

Usage

Load package.

library(DealGPL96)

You can put your own GSE*_RAW.tar under the working directory, now we download one online and test! First running this package, you need to keep your device online.

GEOquery::getGEOSuppFiles("GSE5007", makeDirectory = FALSE, baseDir = tempdir())
file <- list.files(path = tempdir(), pattern = "GSE5007_RAW.tar", full.names = TRUE)
file
result <- DealGPL96(file = file)
result[1:5, 1:3]

When type is "probeID"~

result <- DealGPL96(file = file, type = "probeID")
result[1:5, 1:2]

And when type is "geneSymbol"~

result <- DealGPL96(file = file, type = "geneSymbol")
result[1:5, 1:2]

Details

For the gene symbols corresponding many probes, we take the median of those probes' expression values as the corresponding gene symbol's expression value.

AweKevin/DealGPL96 documentation built on Feb. 9, 2020, 12:12 a.m.