kooperberg: Kooperberg Model-Based Background Correction for GenePix data

Description

This function uses a Bayesian model to background correct GenePix microarray data.

Usage

kooperberg(RG, a=TRUE, layout=RG$printer, verbose=TRUE)

Arguments

an RGList of GenePix data, read in using read.maimages, with other.columns=c("F635 SD","B635 SD","F532 SD","B532 SD","B532 Mean","B635 Mean","F Pixels","B Pixels").

logical. If TRUE, the 'a' parameters in the model (equation 3 and 4) are estimated for each slide. If FALSE the 'a' parameters are set to unity.

layout

list containing print layout with components ngrid.r, ngrid.c, nspot.r and nspot.c. Defaults to RG$printer.

verbose

logical. If TRUE, progress is reported to standard output.

Value

R: matrix containing the background adjusted intensities for the red channel for each spot for each array
G: matrix containing the background adjusted intensities for the green channel for each spot for each array
printer: list containing print layout

Details

This function is for use with GenePix data and is designed to cope with the problem of large numbers of negative intensities and hence missing values on the log-intensity scale. It avoids missing values in most cases and at the same time dampens down the variability of log-ratios for low intensity spots. See Kooperberg et al (2002) for more details.

kooperberg uses the foreground and background intensities, standard deviations and number of pixels to compute empirical estimates of the model parameters as described in equation 2 of Kooperberg et al (2002).

References

Kooperberg, C., Fazzio, T. G., Delrow, J. J., and Tsukiyama, T. (2002) Improved background correction for spotted DNA microarrays. Journal of Computational Biology 9, 55-66.

Ritchie, M. E., Silver, J., Oshlack, A., Silver, J., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. K. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23, 2700-2707. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm412

Examples

Run this code

#  This is example code for reading and background correcting GenePix data
#  given GenePix Results (gpr) files in the working directory (data not
#  provided).
## Not run: 
# # get the names of the GenePix image analysis output files in the current directory
# genepixFiles <- dir(pattern="*\\.gpr$")
# RG <- read.maimages(genepixFiles, source="genepix", other.columns=c("F635 SD","B635 SD",
#                     "F532 SD","B532 SD","B532 Mean","B635 Mean","F Pixels","B Pixels"))
# RGmodel <- kooperberg(RG)
# MA <- normalizeWithinArrays(RGmodel)
# ## End(Not run)

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