Contents
The
GEO to PCL
Conversion allows you to generate a PCL (pre-clustering) file from
one or more NCBI GEO Series accessions. GEO stands for the "Gene
Expression Omnibus" which is a repository of gene expression data
stored
at NCBI. A
GEO
Series defines a set of related
Samples and provides
a summary description for a study. Series also
contain
Platform data describing the array used in the
experiment. A Series accession is formatted
GSExxx
where
xxx is a number, for example, GSE715. A study can be
comprised of more than one Series record, which might or might not be
consecutive in number. A single PCL file is created from all the GEO
Series that you specify. Multiple values for the same clone in the
same Sample are averaged.
Specifying GEO Series Accessions
You
specify GEO Series accessions by entering them, one per line and/or by
specifying a range, say from GSE715 to GSE737. You then provide an
organism, name and description for annotation of the resulting PCL
file which will placed in your repository. After you press submit,
your job request will go into a queue and you will be notified by
email when the PCL file has been created and entered into your
repository. The email will direct you to a temporary log file which
will contain information such as the actual accessions used to
generate the PCL file (in case a range did not contain consecutive
accessions), any problems with the GEO data such as incomplete data
lines.
