Cumbers:Software: Difference between revisions
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[[Image:Screen_shot_2011-08-09_at_3.42.00_PM.png|650px]] | [[Image:Screen_shot_2011-08-09_at_3.42.00_PM.png|650px]] | ||
You can download the files here and run them in R | You can download the files here and run them in R. | ||
1.http://openwetware.org/images/e/e6/Script_to_produce_growth_data_from_single_wells_with_stats_for_a_single_plate_9.0.1.R | 1.http://openwetware.org/images/e/e6/Script_to_produce_growth_data_from_single_wells_with_stats_for_a_single_plate_9.0.1.R | ||
2.http://openwetware.org/wiki/Image:Function_takes_plate%2C_well%2C_returns_growth_stats.3.1.0.R | 2.http://openwetware.org/wiki/Image:Function_takes_plate%2C_well%2C_returns_growth_stats.3.1.0.R | ||
3.http://openwetware.org/images/0/0f/List_wells_from_well_phrase_and_validate_functions.2.2.1.R | 3.http://openwetware.org/images/0/0f/List_wells_from_well_phrase_and_validate_functions.2.2.1.R | ||
'''Instructions for use: | |||
'''You should first create a mySQL database to hold your data, modify the first script to include the information to connect to this. You should then create lookup tables to hold the series data that you eventually want to plot. For example, strain name, location isolated from, date of experiment etc. After this you can run the first script with the XML file from the plate reader. | |||
These scripts have been written for a particular function of automatically reading growth curves from 96 well plates, so please feel free to email me if you have any questions about usage, if any of the notation is not clear or if you would like to adapt this code for another use. | These scripts have been written for a particular function of automatically reading growth curves from 96 well plates, so please feel free to email me if you have any questions about usage, if any of the notation is not clear or if you would like to adapt this code for another use. | ||
Revision as of 16:00, 9 August 2011
Here are some R scripts that I wrote for processing growth curve data from 96 well plates using XML files from a Molecular Devices Plate Reader. There are 7 functions in 3 different files and the diagram below outlines what each function does.
You can download the files here and run them in R. 1.http://openwetware.org/images/e/e6/Script_to_produce_growth_data_from_single_wells_with_stats_for_a_single_plate_9.0.1.R 2.http://openwetware.org/wiki/Image:Function_takes_plate%2C_well%2C_returns_growth_stats.3.1.0.R 3.http://openwetware.org/images/0/0f/List_wells_from_well_phrase_and_validate_functions.2.2.1.R
Instructions for use:
You should first create a mySQL database to hold your data, modify the first script to include the information to connect to this. You should then create lookup tables to hold the series data that you eventually want to plot. For example, strain name, location isolated from, date of experiment etc. After this you can run the first script with the XML file from the plate reader.
These scripts have been written for a particular function of automatically reading growth curves from 96 well plates, so please feel free to email me if you have any questions about usage, if any of the notation is not clear or if you would like to adapt this code for another use.
