[BioC] GEOquery and different types of GPL annotation files

Peter bioconductor-mailinglist at maubp.freeserve.co.uk
Fri Jan 20 15:27:23 CET 2006

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:


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:


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


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



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

More information about the Bioconductor mailing list