Using GEOquery to download multiple expression data series files and then combine

Question

[kmyers2]

I need to combine all available expression data for a number of bacterial species. I have written a python script that can download all the relevant files from GEO for each species. However, when I look at the different series files, often the gene IDs are different. In order to combine all the data together, I will need to have the same gene ID for each series data set. I know I can download the platform files and link them, but that seems inefficient.

Is there a way to modify the geo series file to include a specific (or all) gene ID using GEOquery (or anything else available that you know of) so that when I export it, I can easily combine multiple series files into one by linking the gene IDs?

Answer 1

[Kevin Blighe]

There is not a way to do this with GEOquery. Your best option will be to 'harmonise' the gene IDs using biomaRt.

Kevin