[BioC] GEOquery GSElimits

[James F. Reid]

Dear list,

I can't seem to get the GSElimits parameters of the GEOquery getGEO 
function to work, it seems to be ignored as the full dataset is always 
returned.

Many thanks.
James.

library("GEOquery")

softFile <- system.file("extdata/GSE781_family.soft.gz", package = 
"GEOquery")

## full set
gse <- getGEO(filename = softFile)
Parsing....
Found 36 entities...
GPL96 (1 of 36 entities)
GPL97 (2 of 36 entities)
GSM11805 (3 of 36 entities)
etc..

## reduced set (samples 1 to 5)
gseSub <- getGEO(filename = softFile, GSElimits = c(1, 5))
Parsing....
Found 36 entities...
GPL96 (1 of 36 entities)
GPL97 (2 of 36 entities)
GSM11805 (3 of 36 entities)
etc..


length(names(GSMList(gse)))
[1] 34
length(names(GSMList(gseSub)))
[1] 34

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=en_US.utf8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  tools     methods
[8] base

other attached packages:
[1] GEOquery_2.16.1 Biobase_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.5-0 XML_3.2-0