Bioinformatics - Level 1 Module 2 - Nikita Krishnan

Technical Areas:

  • Filtered Data from txt file to get classes

  • Refreshed how to import data into RStudio from different file sources

  • Created GitHub Account Tools:

  • RStudio

  • Posted instructions about Metadata and function to read CSV

Soft Skills:

  • Critical Thinking: During this lesson, I had to think about how I could most logically organize the metadata to get good classification of different patients and their values.

  • Organization: I had to think about how I want to save each file to allow for easy import into RStudio.

Three Achievement Highlights:

  • Determining batch numbers in a logical and systematic manner

  • Learned about the affy package

  • Determined which characteristics of each patient in the metadata are unique and relevant and thus should be saved

Tasks Completed:

  • First, I downloaded the data. Because I have a Windows computer, I had to download special software to unzip the files.

  • Then I opened the txt file in excel, and then I looked carefully at the different characteristics. I determined that the location was the best way to differentiate different groupings of data, and so I filtered the list into 5 classes. This took a while and I ran into the issue of not knowing how to do this quickly, but I addressed this by using if statements to determine which class each patient belongs in.

  • I determined which metadata characteristics to keep, including size, description, and relation.

  • I then imported this metadata as well as the actual data values into RStudio. I merged affy objects. This went smoothly.