使用Bioconductor下载GEO（Gene Expression Omnibus）上的数据

最新推荐文章于 2025-08-31 15:13:59 发布

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最新推荐文章于 2025-08-31 15:13:59 发布 · 7k 阅读

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本文展示了如何在R中使用Bioconductor包GEOquery从Gene Expression Omnibus（GEO）下载GSE46106数据集，进行初步的数据处理，包括获取表达矩阵、加载NCBI平台注释，并对数据进行预处理。通过示例代码，解释了如何下载原始CEL文件并使用affy包进行表达值计算。

library(GEOquery)
gset <- getGEO("GSE46106", GSEMatrix =TRUE)

Found 1 file(s)
GSE46106_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46106/matrix/GSE46106_series_matrix.txt.gz'
ftp data connection made, file length 4110183 bytes
opened URL
==================================================
downloaded 3.9 Mb

File stored at:
/var/folders/n4/11sc2xz13k56hl85z_h2rgq00000gn/T//RtmpBFQdpL/GPL570.soft

length(gset)

gset <- gset[[1]]

head(pData(gset)[,1:5])

load NCBI platform annotation

gpl <- annotation(gset)

platf <- getGEO(gpl, AnnotGPL=TRUE)

File stored at:
/var/folders/n4/11sc2xz13k56hl85z_h2rgq00000gn/T//RtmpBFQdpL/GPL570.annot.gz
There were 30 warnings (use warnings() to see them)

ncbifd <- data.frame(attr(dataTable(platf), "table"))
eset <- exprs(gset)
head(eset[,1:5])
GSM1123782 GSM1123783 GSM1123784 GSM1123785 GSM1123786
1007_s_at 10.1689 10.5247 10.8179 10.3539 10.4964
1053_at 9.6002 7.9436 9.8653 9.9733 10.1960
117_at 5.6808 5.0301 3.7654 2.7751 2.8179
121_at 4.2268 4.6148 4.6147 4.4977 4.6147
1255_g_at 2.1869 2.1869 2.1869 2.1869 2.1869
1294_at 2.1874 2.1874 2.1874 2.1874 2.1874

head(ncbifd[,1:5])
&nbs