Plate Intensity Image

Description

A function that displays the image of intensity of each well in a plate.

Usage

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imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", sourcePlateName = NA)

Arguments

data.df

The data for all plates including at least five columns for intensity, plate names, well names, rows and columns, respectively.

intensityName

Name of the column in data.df indicating intensities in a plate.

plateName

Name of the column in data.df indicating plate names.

wellName

Name of the column in data.df indicating well types.

rowName

Name of the column in data.df indicating row numbers in a plate.

colName

Name of the column in data.df indicating column numbers in a plate.

sampleName

Name in well types indicating sample names.

sourcePlateName

Name of the column in data.df indicating soure plate names.

Author(s)

Xiaohua Douglas Zhang & Zhaozhi Zhang

References

Zhang XHD, Zhang ZZ. 2013. displayHTS: a R package displaying data and results from high-throughput screening experiments. Bioinformatics (submitted).

Zhang XHD, 2011. Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi Research. Cambridge University Press, Cambridge, UK.

Zhang XHD, 2008. Novel analytic criteria and effective plate designs for quality control in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 363-377.

Zhang XHD, Espeseth AS, Johnson E, Chin J, Gates A, Mitnaul L, Marine SD, Tian J, Stec EM, Kunapuli P, Holder DJ, Heyse JF, Stulovici B, Ferrer M. 2008. Integrating experimental and analytic approaches to improve data quality in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 378-389.

See Also

imageDesign.fn, dualFlashlight.fn, plateWellSeries.fn

Examples

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   data(HTSdataSort)
   par( mfrow=c(4, 3) )
   imageIntensity.fn(data.df=HTSdataSort, intensityName="log2Intensity",
                      plateName="BARCODE", wellName="WELL_USAGE",
                      rowName="XPOS", colName="YPOS", 
                      sampleName="Sample", sourcePlateName="SOBARCODE" )