Problem: How To Add Data to an Existing Study
Topic: caIntegrator Usage
Date entered: 08/25/2011
Release: Up to caIntegrator 1.3
Solution
This guide shows how to add clinical annotation and genomic microarray data to an existing study in caIntegrator, with a focus on common obstacles and pitfalls that may arise in the process. It assumes that you already have basic familiarity with the program and have created a study containing at least one source for both annotation and array data. It also assumes that you have additional sources available, namely:
- Your clinical annotations in the form of a comma delimited text (CSV) file containing at least one field with unique IDs for each subject
- The host name of the caArray server where your data is stored, plus the experiment ID (if you set the data as private, you will also need the user name and password for accessing the data)
- Another two CSV files – a 'mapping file' that maps the subject IDs in your annotations to their corresponding sample IDs in caArray, and a 'control training file' that lists the sample IDs of all control subjects
The guide is presented in a step-by-step instructional format, with each step accompanied by a screenshot from caIntegrator. A hyperlinked index of all the steps appears below.
Getting Started
Loading Additional Clinical Data
Querying Clinical Data
Loading Another Genomic Dataset
Querying Array and Mapping Data
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