In R, how to map gds ids to gse ids

Question

[Zhilong Jia]

How to map gds ids to gse ids in R? There are lots of GDS. As we know, a GDS must have a GSE.

Answer 1

[Sean Davis]

The GEOmetadb bioconductor package can do this for all GDS if you like:

library(GEOmetadb)
sfile = getSQLiteFile()
con = dbConnect(SQLite(),sfile)
dbGetQuery(con,'select gds,title,gse,gpl from gds')

This results in (first 10 rows only):

     gds                                        title    gse   gpl
1   GDS5    Diurnal and circadian-regulated genes (I)   GSE4 GPL13
2   GDS6            Germline development and function   GSE5 GPL14
3  GDS10    Type 1 diabetes gene expression profiling  GSE11 GPL24
4  GDS12               Bone marrow stromal cell lines GSE463 GPL44
5  GDS15 Heat shock from various temperatures to 37°C  GSE18 GPL51
6  GDS16     Heat shock from 25°C to 37°C time course  GSE18 GPL51
7  GDS17                   Hydrogen peroxide response  GSE18 GPL51
8  GDS18           Stationary phase time course (y12)  GSE18 GPL52
9  GDS19               Nitrogen depletion time course  GSE18 GPL52
10 GDS20              Hyper-osmotic shock time course  GSE18 GPL52