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Question: getGEO problem
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gravatar for Sean Davis
8.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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/GSE1002 5-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/R tmpbNUS8Z/GPL6321.soft')) > ? this works > > > > GSE10025.GPL6321<-getGEO(filename='C:/DOCUME~1/IGSPuser/LOCALS~1/Tem p/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
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