How to use
What is ARGEOS doing? It takes your queries and routes them to two different databases: GEO and ArrayExpress. Some of the records in these two databases overlap, but ARGEOS is aware of this and only provides you with unique records. After a query in the first stage, ARGEOS builds a table. At the second stage, ARGEOS provides a complete spreadsheet with all the information required for analysis. This spreadsheet can be downloaded and analyzed via Microsoft Excel, Google sheets, etc.
To get started, go to the page Getting Started. To do this, you can use the buttons in the menu bar (top). On this page there are request fields and a field where you can specify the mail (optional). If you indicated your mail, then we can send you a letter at the end of the work. You can also subscribe to updates: after a specified period of time, ARgeos will send you new data that has appeared in the databases.
2) How to compose a request
We recommend starting with a list of keywords. Think what words In the field "your request" you should enter keywords, which will be searched for in all fields.
3) Query analysis
When you are confident that your search queries are configured correctly, you can run a basic analysis. To do this, simply click on the "continue analysis" button. Pay attention to the checkbox "do not break lines". Sometimes researchers conduct an experiment with several species or take different measurements (RNA-seq and ChiP seq). However, they can publish data in one record. By default, ARGEOS splits such records into several, providing convenient filtering. However, if you need such information to be presented in one line, put a tick in this field.
When the analysis is over, the status of the work will change to "ready" You can download the spreadsheet and analyze it through Microsoft Excel, Google Sheets, and other programs. Let's consider the most affordable option, analysis through Google sheets.
4) Analysis of the table
Let's proceed to the most important thing - the analysis of the final table. For convenience, you can freeze the first line. You can sort by fields of interest (do not forget to indicate that the column is with a heading). We advise you to start by sorting by experiment type and filtering only by the types you are interested in.
If your query includes someone's last name, you might want to look at the column of author names (use a range search). For example, for the query "Parkinson's disease" there maybe works from another field, but which were completed by a person with the surname Parkinson.
A few tips:
Do not fully trust the information recorded in GEO.
This information is entered manually. Accordingly, errors are possible in it, sometimes significant. For example, sometimes you come across data where researchers forgot to change the protocol and inadvertently left the protocol for another study. Try to check information on key cells: name, summary. Also, the summary articles are always helpful. If there are a lot of factual errors in the record and there is no detailed information, think about it, do you need it? Perhaps such information simply cannot be re-analyzed. protocols specified in articles.
Why doesn't ARGEOS have a built-in tool for working with a table / you haven't made a tool for working with data?
First, it would increase the load on our servers. Secondly, the functionality of third-party programs (Excel) fully covers all the necessary working tools. Why invent something if it already exists? In addition, this way you can be sure that all your changes have been saved and not lost due to an accidental error. You do backups, right? :)