[BioC] GEOquery and different types of GPL annotation files

[Peter]

Do anyone know what the difference is between these two GEO GPL files?

GPL199.annot (540kb)
GPL199.soft (2166kb)

I downloaded the GPL199.annot file here, as far as I can tell it is the 
only file available on the FTP site with GPL199 in the name:

ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_platform/annot/GPL199.annot.gz

If you browse a GDS file using this platform, e.g. GDS680, and click on 
the download icon and select "Annotation SOFT file" you also end up at 
the same GPL199.annot.gz file:

http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi?gds=680

On the other hand, GEOquery downloaded GPL199.soft from here:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL199&form=text&view=full

It seems that GEOquery will load GPL199.soft happily, but fails on 
GPL199.annot (and other GPL*.annot files) like so:

 > gpl <- getGEO(filename="c:/temp/geo/GPL199.annot")
Error in switch(as.character(first.entity[1]), sample = { :
         argument is missing, with no default


Thanks

Peter

P.S. Sean - Thanks for fixing the problem with missing geneNames in 
GEOquery_1.5.3