下载GSE
rm(list = ls())
library(GEOquery)
Data <- getGEO("GSE63310",destdir = "./") # 不写destdir，下载到tmp，而不是getwd()
# 默认getGPL = TRUE
# 下载结果：GSE63310_series_matrix.txt.gz；GPL13112.soft
data=getGEO(filename = "GSE63310_series_matrix.txt.gz")
下载GPL数据
> gpl13112=getGEO("GPL13112",destdir = "./")
# Using locally cached version of GPL13112 found here:.//GPL13112.soft
> names(Meta(gpl13112))
[1] "contact_country" "contact_name" "data_row_count"
[4] "distribution" "geo_accession" "last_update_date"
[7] "organism" "sample_id" "series_id"
[10] "status" "submission_date" "taxid"
[13] "technology" "title"
下载cel数据
library(GEOquery)
tmp=getGEOSuppFiles(GSE63310)
if (is.null(tmp)) {
warning("Supplementary data files not provided!\nyou should check this GEO ID in NCBI\n")
}
下载gsm数据
cat gsm.list
GSM1545535
GSM1545536
GSM1545537
GSM1545538
GSM1545539
GSM1545540
GSM1545541
GSM1545542
GSM1545543
GSM1545544
GSM1545545
cat gsm.list | while read id; do wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1545nnn/$id/suppl/*gz; done
a=read.table("gsm.list")
gz数据
学习bioconductor：http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html#platforms
