Description of functions, workflow and configuration files. For a typical workflow, refer to demo.m
- Authors: Ce Gao
- Created: 2013-05-30
- Revised:
- Toolbox: microplate parser
importAssayData: import data from raw data files, construct structure, uses:
- readPlateList: return featureData
- readPlateConf: read Plateconf file
- readPlateFile: read OD and GFP, import them to assayData, uses:
- importFun: design specific for our data format
data .assayData .OD: an array, zeros(nTotalWells, nTime) .GFP: an array, zeros(nTotalWells, nTime) .featureData: Note: all fields below are vectors of size (nTotalWells,:) .plate: plate serial number .layout: layout type .repPlate: plate replicates .control: containing type of control in the well .chemical: different chemical .conc: different chemical concentration .gene: genes .pathway: pathway .metaData .dataPath: directory the data/conf files .plateConfFile: plate configuration file name .plateListFile: plate list file name .dataFiles: cell(nPlates,1), data file names .nPlates: total plate number .nLayout: distinct plate types .nWells: well number on each plate .nTotalWells: nWells*nPlates .nTimePoints: time points .timeCreated: time .lastModified: time .lastAccessedBy: function name - Layout: different plate layouts, (wca.featureData.layout);
- Replicate: experimental replication,(wca.featureData.replicate);
- Chemical: denotes different toxicant,(wca.featureData.chemical)
The first 2 lines are shown:
Filename Layout Replicate Chemical BaP.txt 1 1 1 - Wells: total well number on a single plate
- Layouts: total types of unique layouts
- TimePoints: number of time points sampled
- Layout: types of layout
- Well: well number on the plate
- ControlStatus: sample control status
- Gene
- Pathway
- Concentration
The first 6 lines are shown here:
Wells: 60 Layouts: 2 TimePoints: 10 Layout Well ControlStatus Gene Pathway Concentration 1 A01 NA NA NA -1 1 A02 media NA NA 0