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
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