[BioC] getGEO problem

[Sean Davis]

On Tue, Feb 9, 2010 at 5:01 PM, Vladimir Grubor <vg37 at duke.edu> wrote:
> Hi Sean,
>
>
>
> First I want to compliment you on the excellent package GEOquery. I’ve been
> using it to look at some aCGH data.
>
> I updated my R from 2.9.2 to 2.10.1 and now I’m having problems with my
> queryies:
>
>
>
> GSE10025.GPL6321<-getGEO(filename='E:/temp/ncbi_geo/GSE10025/GSE10025-GPL6321_series_matrix.txt.gz',GSEMatrix=TRUE,AnnotGPL=TRUE)
>
> Error in switch(as.character(first.entity[1]), sample = { :
>
>   argument is missing, with no default
>
>
>
> I was able to execute this in 2.9.2 (I’m not sure which version of
> Bioconductor I had).
>
> I looked online and found your suggestions of downloading everything from
> scratch:
>
>
>
> GSE10025<-getGEO(GEO="GSE10025",GSEMatrix=TRUE,AnnotGPL=FALSE)
>
>
>
> GPL6321<-Table(getGEO(filename='C:/DOCUME~1/IGSPuser/LOCALS~1/Temp/RtmpbNUS8Z/GPL6321.soft'))
> – this works
>
>
>
> GSE10025.GPL6321<-getGEO(filename='C:/DOCUME~1/IGSPuser/LOCALS~1/Temp/RtmpbNUS8Z/GSE10025-GPL6321_series_matrix.txt.gz')
>
> Error in switch(as.character(first.entity[1]), sample = { :
>
>   argument is missing, with no default
>
>
>
> Same thing! Importing the whole GSE does not work with this dataset as it’s
> too big (multiple samples on multiple GPLs).
>
> Can you please help me with this?

Hi, Vladimir.  I had made some changes in the last release cycle that
broke GSEMatrix filename-based parsing.  I think the fix is in place
now in the Bioc 2.5 release.  It should take a day or two to become
available via biocLite().  The GEOquery version will need to be 2.11.3
(or greater).

> Also, I’m still not sure what the AnnotGPL function does. Can you please
> clarify it for me?

As for the AnnotGPL, GEO maintains two GPL records for any data that
become GDS records.  The Annotated GPL is curated by NCBI GEO to have
standard columns.  In some cases, it is nice to have the
standard columns, but the original GPL records sometimes have
important ancillary columns that get removed when they become
Annotated GPLs.  The only time this parameter is used is when a GDS
record is being fetched.

Sean