[BioC] GEOquery error importing GEO data with 'null' values

[Dreyfuss, Jonathan]

When getGEO() parses a GSEMatrix, I frequently receive a scan() error. For
instance, 

> eset <- getGEO(GEO="GSE1755", destdir=getwd(), GSEMatrix=TRUE)

downloads without error, but then:

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  scan() expected 'a real', got 'null'
In addition: Warning messages:
1: In if (nchar(val) == nchar(x)) return(NA) :
  the condition has length > 1 and only the first element will be used
2: In if (nchar(val) == nchar(x)) return(NA) :
  the condition has length > 1 and only the first element will be used
3: In if (nchar(val) == nchar(x)) return(NA) :
  the condition has length > 1 and only the first element will be used

I have not been able to resolve this question by searching google or this list,
but I have noticed that GEO often has "null" values where R expects "NA". It
seems to me that one option may be for GEOquery to use scan() with argument
na.strings=c("NA", "null").

thanks for the help and the wonderful software,
jonathan

> sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_
MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
C_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] GEOquery_2.4.0 RCurl_0.9-3    Biobase_2.0.1

----------------------
jonathan dreyfuss
bioinformatics analyst
harvard partners center for genetics and genomics


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