Script to reformat data from a 96-well Plate Fluorescence Spectrophotometer (Plate Reader) to facilitate analysis.
This ipython notebook takes output data from a 96-well Plate Fluorescence Spectrophotometer, and reorganizes and summarizes the data so that chemists can more easily analyze for patterns.
The original output data from a Plate Reader is a text file that approximates the layout of the well-plate. This notebook script transforms the data to output two new files.
Users can specify different numbers for well_groupings which map to compounds in the output data, and relabel compounds and row concentrations to more accurately identify the values.
37.00 4.4886 0.74 0.7452 0.7466 0.74 0.746 0.7412 0.744 0.7438 0.7462 0.7474 0.7432
3689.802 3409.322 3778.041 3079.057 2818.387 2788.283 2845.285 3284.842 3649.555 3456.887 3660.852 3742.566
The first value (37.00) is a temperature reading. The subsequent values in the first row are time readings. The second row contains corresponding fluorescence readings for each time. This is repeated for each row in the plate, with a break in between.
| PlateRead | Concentration | Compound | Time | Fluorescence | |
|---|---|---|---|---|---|
| 0 | 1 | Control | Compound A | 0.7386 | 3689.802 |
| 1 | 1 | Control | Compound A | 0.74 | 3409.322 |
| 2 | 1 | Control | Compound A | 0.7452 | 3778.041 |
| 3 | 1 | Control | Compound A | 0.7466 | 3079.057 |
| 4 | 1 | Control | Compound B | 0.74 | 2818.387 |
| 5 | 1 | Control | Compound B | 0.746 | 2788.283 |
| 6 | 1 | Control | Compound B | 0.7412 | 2845.285 |
| 7 | 1 | Control | Compound B | 0.744 | 3284.842 |
| 8 | 1 | Control | Compound C | 0.7438 | 3649.555 |
| 9 | 1 | Control | Compound C | 0.7462 | 3456.887 |
| 10 | 1 | Control | Compound C | 0.7474 | 3660.852 |
| 11 | 1 | Control | Compound C | 0.7432 | 3742.566 |
(same data as above, formatted to show each well-reading individually)
| Plate Read | Concentration | Compound | Avg Fluorescence | Standard Deviation | Avg Time | |
|---|---|---|---|---|---|---|
| 21 | 1 | Control | Compound A | 3489.0555 | 315.3135886 | 0.7426 |
| 22 | 1 | Control | Compound B | 2934.19925 | 234.9185045 | 0.7428 |
| 23 | 1 | Control | Compound C | 3627.465 | 121.0340918 | 0.74515 |
(further groups data by plate, row, and compound, and provides average stats)
To make it easier to analyze the output data for active compounds, and create charts for research.
Python 2.7 Required packages: csv, pandas, numpy, decimal