LPE (version 1.46.0)

baseOlig.error: Evaluates LPE variance function of M for quantiles of A within and experimental condition and then interpolates it for all genes.

Description

Calls baseOlig.error.step1 and baseOlig.error.step2 functions in order to calculate the baseline distribution.

Usage

baseOlig.error(y, stats=median, q=0.01, min.genes.int=10,div.factor=1)

Arguments

y

y is a preprocessed matrix or data frame of expression intensities in which columns are expression intensities for a particular experimental condition and rows are genes.

stats

It determines whether mean or median is to be used for the replicates

q

q is the quantile width; q=0.01 corresponds to 100 quantiles i.e. percentiles. Bins/quantiles have equal number of genes and are split according to the average intensity A.

min.genes.int

Determines the minimum number of genes in a subinterval for selecting the adaptive intervals.

div.factor

Determines the factor by which sigma needs to be divided for selecting adaptive intervals.

Value

Returns object of class baseOlig comprising a data frame with 2 columns: A and var M, and rows for each quantile specified. The A column contains the median values of A for each quantile/bin and the M columns contains the pooled variance of the replicate chips for genes within each quantile/bin.

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.

Jain et. al. (2005) Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data, BMC Bioinformatics, Vol 6, 187.

See Also

lpe

Examples

  # Loading the library and the data
  library(LPE)
  data(Ley)
  
  dim(Ley)
  # Gives 12488 by 7
  Ley[1:3,]
   # Returns 
  #       ID           c1   c2   c3    t1    t2    t3
#   1  AFFX-MurIL2_at 4.06 3.82 4.28 11.47 11.54 11.34
#   2 AFFX-MurIL10_at 4.56 2.79 4.83  4.25  3.72  2.94
#   3  AFFX-MurIL4_at 5.14 4.10 4.59  4.67  4.71  4.67

  Ley[,2:7] <- preprocess(Ley[,2:7],data.type="MAS5")
  
  subset <- 1:1000
  Ley.subset <- Ley[subset,]
  
  # Finding the baseline distribution of subset of the data
  # condition one (3 replicates)
  var.1 <- baseOlig.error(Ley.subset[,2:4], q=0.01)
  dim(var.1)
  # Returns a matrix of 1000 by 2 (A,M) format, equal to the nrow(data)