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_A DDRESS=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 The information transmitted in this electronic communica...{{dropped:16}}

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