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(es