[BioC] getGEO function to load files from other locations than GEO ?

[Sean Davis]

Wolfgang Raffelsberger wrote:
> Dear list,
>
> Sorry to bug you again on the issue of using the "getGEO()" function
> to load files from other locations than GEO...
>
> Sean Davis a écrit :
>> See the help for getGEO.  There is a filename argument that does
>> exactly what you are describing. 
>> Sean
>>   
>
> I tried to spicify the file using the filname-argument :
>
> > in.file <- "GSM180487.txt"             # just picking an example of
> an original GEO downloaded &decompressed file
> > deGEO1 <- getGEO(filename=in.file )      # i.e., from the directory
> with my file...
> Error in switch(as.character(first.entity[1]), sample = { :
>        argument is missing, with no default
Wolfgang,

It looks like GSM180487 might not be a SOFT format file.  If you run
this command:

readLines('GSM180487.txt',n=10)

you should get this:

 [1] "^SAMPLE = GSM180487"
 [2] "!Sample_title = ACC 1"
 [3] "!Sample_geo_accession = GSM180487"
 [4] "!Sample_status = Public on Apr 10 2007"
 [5] "!Sample_submission_date = Apr 04 2007"
 [6] "!Sample_last_update_date = Apr 09 2007"
 [7] "!Sample_type = genomic"
 [8] "!Sample_channel_count = 2"
 [9] "!Sample_source_name_ch1 = ACC Tumor Sample 1"
[10] "!Sample_organism_ch1 = Homo sapiens"

If not, then you don't have a SOFT format file, most likely.  Let me
know if you need more direction.

Sean