Biotech7005

Assignment 1 - 27 Marks

Due before 5pm, Tuesday 13th August, 2019

Your answers to all questions should be submitted to myUni as a single R markdown file with the file suffix .Rmd. [1 mark]

• A compiled html, MS Word or PDF document is not required, but will be generated when marking.[1 mark]
• Ensure your submitted file begins with your student number. [1 mark]
• Add appropriate text and/or comments making your thoughts clear to any collaborators. [2 marks]

Obtaining Your Data

All data is in the file available here. Please extract the complete set of files, and use the file labelled with your student id. Do not change the name of the file you obtain, but continue to work with this file as a1xxxxxx.csv.

Please note that R Markdown will require this file to be in the same directory as the markdown file itself is in. Your file can be uploaded to your VM using the Upload button in the RStudio Files pane. We strongly suggest creating a directory called Assignment_1 on your VM and placing both your RMarkdown and your file in this directory.

Tasks in R

1. Load your allocated file removing all comments, blank rows and changing any encoded missing values to NA. [4 marks]
2. Extract the CellType and Treatment information from the sample names, placing them in separate columns after converting from wide to long form. [4 marks]
3. Create a correctly labelled boxplot of your dCt values for each of the four conditions. [4 marks]
4. Conduct a simple linear regression on your data using the model dCt~CellType + Treatment + CellType:Treatment and include the model output from the function summary() without interpretation. [2 marks]

Research questions

Please answer on the same *.Rmd file as the first section, using a new markdown heading for this section.

1. Two common file types are .csv and .tsv. What is the difference between the two, and can you suggest a function for loading a .tsv file into R? [3 marks]
2. Three types of message commonly seen in the R Console are 1) error messages, 2) warnings and 3) general messages. Briefly describe the importance of each type of message and what information they are conveying. [3 marks]
3. What is the difference between an integer and a floating point value? Floats are sometimes called “doubles”. What does this mean? [2 marks]