knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
GEO provides a wealth of biology related data, and GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array) is one of the the most common biological chip platform.Although the post-processed matrix data are always provided, but the RAW data are most convincing! Here we developed to deal GPL570 RAW.tar file using the robust multi-array average expression measure, and returns data frame which is expression profile. Plus: DealGPL570 function can filter cels which are not of GPL570 platform in the RAW.tar file.
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("GSE104683", makeDirectory = FALSE, baseDir = tempdir()) file <- list.files(path = tempdir(), pattern = "GSE104683_RAW.tar", full.names = TRUE) file result <- DealGPL570(file = file) result[1:5, 1:3]
When type is "probeID"~
result <- DealGPL570(file = file, type = "probeID") result[1:5, 1:2]
And when type is "geneSymbol"~
result <- DealGPL570(file = file, type = "geneSymbol") result[1:5, 1:2]
For the gene symbols corresponding many probes, we take the median of those probes' expression values as the corresponding gene symbol's expression value.
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