preprocess {LPE}R Documentation

Preprocessing the data (IQR normalization, thresholding, log- transformation, and lowess normalization)

Description

Finds inter-quartile range of the data = (75th percentile - 25th percentile), thresholds low intensity MAS4, MAS5 and dChip data to 1, then log transforms the data (base 2), and dows lowess normalization

Usage

  preprocess(x, data.type="MAS5",threshold=1,LOWESS=TRUE)

Arguments

x x is the data-set which needs preprocessing.
data.type Three types of data accepted in the current version : MAS4 (Microarray suite software) , MAS5 and dChip
threshold threshold is the 'thresholding value' below which all data would be thresholded (default = 1).
LOWESS LOWESS is a logical variable which determines if lowess normalization needs to be performed.

Value

Returns a data-set of same dimensions as that of the input data. It has IQR normalization for MAS4 and MAS5 data. Low intensities of MAS4, MAS5 and dChip data are thresholded to 1. Then data is transformed to base 2, and finally lowess based normalization is applied.

References

J.K. Lee and M.O.Connell(2003). An S-Plus library for the analysis of differential expression. In The Analysis of Gene Expression Data: Methods and Software. Edited by G. Parmigiani, ES Garrett, RA Irizarry ad SL Zegar. Springer, NewYork.

Jain et. al. (2003) Local pooled error test for identifying differentially expressed genes with a small number of replicated microarrays, Bioinformatics, 1945-1951.

See Also

lpe

Examples

  library(LPE)
  # Loading the LPE library
 
  data(Ley)
  # Loading the data set
  dim(Ley) #gives 12488 * 7
  Ley[1:3,]

  Ley[1:1000,2:7] <- preprocess(Ley[1:1000,2:7],data.type="MAS5",
        threshold=1, LOWESS=TRUE)
  Ley[1:3,]
 

[Package LPE version 1.1.5 Index]