[BioC] illumina beadarray GEO files

Nathalie Conte nac at sanger.ac.uk
Wed Jun 15 14:13:33 CEST 2011


HI
I want to have a look at this experiment which is deposited in GEO under 
the reference:GSM 290549, this experiment contains 6 files
GSM296418.csv.gz 	293.0 Kb 	(ftp) 
<ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM296nnn/GSM296418/GSM296418%2Ecsv%2Egz>(http) 
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM296418&db=GSM296418%2Ecsv%2Egz&is_ftp=true> 
	CSV
GSM296418.locs.gz 	7.2 Mb 	(ftp) 
<ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM296nnn/GSM296418/GSM296418%2Elocs%2Egz>(http) 
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM296418&db=GSM296418%2Elocs%2Egz&is_ftp=true> 
	LOCS
GSM296418.tif.gz 	51.7 Mb 	(ftp) 
<ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM296nnn/GSM296418/GSM296418%2Etif%2Egz>(http) 
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM296418&db=GSM296418%2Etif%2Egz&is_ftp=true> 
	TIFF
GSM296418.txt.gz 	11.4 Mb 	(ftp) 
<ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM296nnn/GSM296418/GSM296418%2Etxt%2Egz>(http) 
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM296418&db=GSM296418%2Etxt%2Egz&is_ftp=true> 
	TXT
GSM296418.xml.gz 	665 b 	(ftp) 
<ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM296nnn/GSM296418/GSM296418%2Exml%2Egz>(http) 
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM296418&db=GSM296418%2Exml%2Egz&is_ftp=true> 
	XML

  I am trying to find a way to reanalyse this, but is struggling to find 
a appropriate way. I just want to know whether the genes in this array 
are below or above the detection level threshold  used in beadarray.
 Has anybody got any advice about a way to  analyse microarray data 
deposited in GEO to get this kind of information?
many thanks
Nat


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