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

[Sean Davis]

On Thu, Jul 3, 2008 at 4:18 PM, Dreyfuss, Jonathan
<JDREYFUSS1 at partners.org> wrote:
> 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, Jonathan, for the suggestion.  This sounded like a great
change, so you will find it in the devel version of GEOquery (2.5.3,
to be exact).  It should be available in the next couple of days as
the build process picks up the change.

Sean