Lab Meeting Information
20160127 - R Script for CFX Quantitation Spreadsheets

Sean wrote an R script:
https://github.com/kubu4/Scripts/tree/master/R

The script transposes replicate Cq data and moves them to a single row.
The script operates on the default quantitation CSV file that can be exported from CFX Manager v.3.0.


20151217 - Web Presence

General Lab Concerns
- End of quarter cleaning day(s)
- Attendance

WordPress (temporary: friedmanlab.wordpress.com)

CONTENT
- Mostly visual
- Large, good looking image at top of page
- Who are we (PI, students, staff, collaborators)?
- People
- General lab interests
- Current projects
- Blog
- Prospective Students Info
- Publications

Potential Themes
- edin
- snaps (photography-based)
- sight (online magazine)
- gateway
- oxygen (dynamic header)

Write up bios (if you don't have one)
Provide "selfie"


20151112 - R Basics

Using R & R Studio

Before Using R Studio - Data formatting
  • Use CSV files
  • Organize data in columns
  • If data in rows -> transpose in spreadsheet to columns
  • Deal with outliers in spreadsheet before R
  • Use column headers (no spaces in header labels)
  • Leave empty data cells empty; don't use "NA"
  • Spreadsheet to CSV -> Save As... (only saves current sheet)
  • Import into R Studio - Don't forget to press "yes" radio button next to Heading

Examples - Basic Histogram
>plot(test$Species, type = "h")
  • plot = command to plot data
  • test = file name
  • $Species = column in file
  • "h" = specifies plot type - in this case histogram; if no type is specified, R will try to automatically generate the correct plot type.

Need internal R help?
Use: ?<command> (Replace <command> with the command you need help with. For example: ?plot

Shapiro-Wilk normality test - This evaluates whether or not a dataset is normally distributed. A low p-value for this indicates a non-normally distributed dataset.
>shapiro.test(rppnew$Metaplasia)
  • shapiro.test = command
  • rppnew = file name to work on



September 2011






April 2011