README.md

In SCIL-leuven/qpcrviia7: qPCR analysis from viia7

qPCR analysis

Package for easy and fast qPCR analysis made especially for data obtained with Viia 7 Real-time PCR system.

UPDATE

• Simplified workflow with less functions
• Added calculation of fold change
• Added statistical analysis (wilcox and t.test)

Install

Install these packages in Rstudio:

install.packages(c("devtools", "tidyverse"))

Installation of qPCR package

devtools::install_github("SCIL-leuven/qPCR")

Data file

Make sure all files are .xlsx files because read_excel has problems with importing .xls files.

Import all the raw data as an excel file without any selections. We are only interested in the results, that is the third sheet. In the basic template on the Viia7, genes are Targets and samples Samples. You can find them under the Sample Name and Target Name column.

Well | Well Position | Sample Name | Target Name | CT -----|---------------|-------------|-------------|---- 1 | A1 | Sample 1 | Gene 1 | 21.23 2 | A2 | Sample 2 | Gene 1 | 24.48 3 | A3 | Sample 1 | Gene 2 | 18.98

Annotation file

To plot groups, you need to create an annotation file (this is the easiest to do in excel but it can also be a .csv or .txt file). Here is an example of how it should look:

Sample Name | Condition | Mouse | ... ----------|-----------|-----------|------ Sample 1 | healthy | a | ... Sample 2 | healthy | b | ... Sample 3 | diseased | a | ...

Workflow

Rmarkdown examples

To check the example analyses run this code in the terminal: devtools::build_vignettes()

You can also run the code chunk by chunk with Rmarkdown. Open an .Rmd file in the folder vignettes and run the chunks by pressing on the green play button top right.

Basic workflow in steps

1. Read and prepare files
2. Quality control
3. Normalize to housekeeping genes
4. Fold change
5. Plotting
6. Statistics
7. Export data

To do

• Add information to load your files in .Rmd examples
• Add more statistics

SCIL-leuven/qpcrviia7 documentation built on May 21, 2019, 2:31 a.m.