[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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