Experiment Overview
| Repository ID: | FR-FCM-ZZ4P | Experiment name: | Dataset 3-Flow Cytometer Sensitivity: A Quadratic Model | MIFlowCyt score: | 43.50% |
| Primary researcher: | Faysal El Khettabi | PI/manager: | Ryan Brinkman | Uploaded by: | Faysal El Khettabi |
| Experiment dates: | 2012-07-01 - 2012-12-25 | Dataset uploaded: | Dec 2012 | Last updated: | Jan 2013 |
| Keywords: | [Flow cytometer sensitivity] | Manuscripts: | |||
| Organizations: |
BC Cancer Agency, Terry Fox Lab, Vancouver, BC (Canada)
|
||||
| Purpose: | Q and B calculation. Dataset 3 was provided by Comprehensive Cancer Center Flow Cytometry Core Facility at Wake Forest University School of Medicine and involved calibrator beads ( Spherotech RCP -30-5A 8 peak beads) run through a BD FACS Aria cytometer using two experiments: (1) Signal attenuation, the emissions from the blue (488nm) laser were attenuated in the green channel (530BP) by using custom annuli cut from black paper. The annuli were laid on photomultiplier side of the 530BP filter and held in place by gravity. The target attenuations were 90\%, 75\% and 25\%. The actual attenuations achieved were 91\%, 70\% and 25\%. The signals in all the other channels were not attenuated. (2) Increased noise levels, a flashlight with in an incandescent light bulb was shined into the area of the flow cell to increase the background light levels. Adjustment of the angle of illumination and distance of the flashlight from the flow cell allowed different levels of background light to enter the measurement area. The background light affected all channels. Background light levels were only qualitatively adjusted and chosen at three arbitrary levels of high, medium and low. Dataset was used to test our R package flowQB's ability to generalize by evaluating its performance on a set of data not used for its modelling and implementation. | ||||
| Conclusion: | None | ||||
| Comments: | Data analysis was conducted using R/BioConductor. We used R’s implementation for K-means clustering to enable the automatic gating and the statistics extraction. The R functions for regression analysis lm was used to fit linear and quadratic regression models. The R function Poly was used to evaluate orthogonal polynomials involved in solving the resulting linear system of equations. We developed a freely available open source R/BioConductor package flowQB to automate the main steps for Q and B calculation, available through CRAN/Bioconductor. It includes a vignette that provides a task-oriented description of its functionality and an executable example that is intended to be used interactively. Thanks to everybody who provided FCS files for this collection! Please email Ryan Brinkman (rbrinkman@bccrc.ca) if you have any questions. | ||||
| Funding: | Not disclosed | ||||
| Quality control: | MESF calibration used p=17493/4286 for voltage 571V Calibrator Mean =4286 and Calibrator Standard Value =17493. | ||||
