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Manual import of data and annotations from GEO
Question
ID
132
Category
Qlucore Omics Explorer
  Data Import
Date Created
2019-09-05 10:04:33
Date Updated
2019-09-05 10:07:21
How do I manually import data and annotations from GEO?
Answer
Downloading and importing manually:

1. Go to https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40589
In case the GEO data set of interest contains both a series matrix file and a SOFT file with annotation (e.g. GSE40589) use this procedure to manually download:

To get the data:
2. From the link on the ncbi page download the series matrix file to any location on your computer (does not need to be the GEO folder, that is only used for the automatic download/import) and unpack it.
3. Open the series matrix file in a text editor and remove the very last line in the file (the line says "!series_matrix_table_end") and save the file.
4. Open Omics Explorer and select File->Open with Wizard, Wizard, and then select the modified series matrix file.
5. Follow the instructions in the wizard to open the data set in Omics. Selecting the data part is straightforward. Regarding sample annotations select those rows that seem relevant for your purposes. I choose !Sample_title" and "!Sample_geo_accession".

To get additional variable annotations:
6. From the link on the ncbi page download the SOFT formatted family file to any location on your computer and unpack it.
7. Open the file in a text editor and remove everything except the part containing the variable annotation rows + their headers and save it as a .txt file. (I have attached the resulting file for convenience.)
8. In Omics Explorer with the GEO data set open go to File->Import->Variable Annotations and open the modified SOFT file from the previous step.
9. Save the data set as a .gedata (File->Save As).
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