GEOmetadb demo; see http://nsaunders.wordpress.com/2010/01/08/samples-per-seriesdataset-in-the-ncbi-geo-database/

GEOmetadb.R

# install GEOmetadb
source("http://bioconductor.org/biocLite.R")
biocLite("GEOmetadb")
library(GEOmetadb)

# connect to database
getSQLiteFile()
con <- dbConnect(SQLite(), "GEOmetadb.sqlite")

# count samples per GDS
gds.count <- dbGetQuery(con, "select gds,sample_count from gds")
gds.count[1:5,]
# first 5 results
     gds sample_count
1   GDS5            5
2   GDS6           29
3  GDS10           28
4  GDS12            8
5  GDS15            6
# count samples per GSE
gse <- dbGetQuery(con, "select series_id from gsm")
gse.count <- as.data.frame(table(gse$series_id))
gse.count[1:10,]
# first 10 results
                Var1 Freq
1               GSE1   38
2              GSE10    4
3             GSE100    4
4           GSE10000   29
5           GSE10001   12
6           GSE10002    8
7           GSE10003    4
8  GSE10004,GSE10114    3
9           GSE10005   48
10          GSE10006   75