Just a quick question: Does anyone have a parser for GEO SOFT format
files
with the goal to bring series into R?
Thanks,
Sean
[[alternative HTML version deleted]]
>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.