[BioC] GEO data extraction

[John Zhang]

>Just a quick question:  Does anyone have a parser for GEO SOFT format files
>with the goal to bring series into R?

There is a parser in the AnnBuilder package. For example: 

> geo <- GEO()
> gsm107 <- queryGEO(GEOObj = geo, GEOAccNum = "GSM107")
> gsm107[1:5,]
     ID_REF SIGNAL_RAW BKD_RAW VALUE   
[1,] "1"    "38687"    "44944" "-6257" 
[2,] "2"    "25525"    "44944" "-19419"
[3,] "3"    "21320"    "44944" "-23624"
[4,] "4"    "22463"    "44944" "-22481"
[5,] "5"    "666534"   "44944" "621590"

where GEOAccNum is the GEO accession number assigned to files by GEO.