[BioC] GEOquery problem

[James W. MacDonald]

Hi David,

David martin wrote:
> It looks to me that there might some problem with softfiles. Did anybody 
> came across a similar problem ??
> 
> 
> library(GEOquery)
> gse <- getGEO(filename = 
> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery"))
> 
> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>   invalid 'nlines' argument
> In addition: Warning messages:
> 1: In file(fname, "r") :
>   file("") only supports open = "w+" and open = "w+b": using the former
> 2: In file(con, "r") :
>   file("") only supports open = "w+" and open = "w+b": using the former
> 3: In file(fname, "r") :
>   file("") only supports open = "w+" and open = "w+b": using the former

You have to point to a file that actually exists!

 > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")
[1] ""

If I use the softfile in that directory, it works for me.

 > gse <- getGEO(filename = 
system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), 
GSEMatrix=FALSE)
Parsing....
Found 36 entities...
GPL96 (1 of 36 entities)
GPL97 (2 of 36 entities)
GSM11805 (3 of 36 entities)
GSM11810 (4 of 36 entities)
GSM11814 (5 of 36 entities)
GSM11815 (6 of 36 entities)
GSM11823 (7 of 36 entities)
GSM11827 (8 of 36 entities)
GSM11830 (9 of 36 entities)
GSM11832 (10 of 36 entities)
GSM12067 (11 of 36 entities)
GSM12069 (12 of 36 entities)
GSM12075 (13 of 36 entities)
GSM12078 (14 of 36 entities)
GSM12079 (15 of 36 entities)
GSM12083 (16 of 36 entities)
GSM12098 (17 of 36 entities)
GSM12099 (18 of 36 entities)
GSM12100 (19 of 36 entities)
GSM12101 (20 of 36 entities)
GSM12105 (21 of 36 entities)
GSM12106 (22 of 36 entities)
GSM12268 (23 of 36 entities)
GSM12269 (24 of 36 entities)
GSM12270 (25 of 36 entities)
GSM12274 (26 of 36 entities)
GSM12283 (27 of 36 entities)
GSM12287 (28 of 36 entities)
GSM12298 (29 of 36 entities)
GSM12299 (30 of 36 entities)
GSM12300 (31 of 36 entities)
GSM12301 (32 of 36 entities)
GSM12399 (33 of 36 entities)
GSM12412 (34 of 36 entities)
GSM12444 (35 of 36 entities)
GSM12448 (36 of 36 entities)

 > sessionInfo()
R version 2.11.0 Patched (2010-05-01 r51890)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] GEOquery_2.12.0 RCurl_1.4-2     bitops_1.0-4.1  Biobase_2.8.0

loaded via a namespace (and not attached):
[1] tools_2.11.0

Best,

Jim



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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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