\name{adjBaseOlig.error.step1}
\alias{adjBaseOlig.error.step1}

\title{
 Evaluates LPE variance function of M for quantiles of A within and experimental condition by divinding the A in 100 intervals.
}

\description{
  Genes are placed in bins/quantiles according to their average
  expression intensity. The function adjBaseOlig.error calculates a 
  pooled variance of M for genes within these bins/quantiles of A 
  for the replicates of the experimental condition contained in y.
  Here the assumption is that variance of the genes in each interval
  is similar.
}

\usage{
  adjBaseOlig.error.step1(y, stats=median, setMax=FALSE, q=0.01, df=10)
}

\arguments{
 \item{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.}
 \item{stats}{It determines whether mean or median is to be used
	  for the replicates}
 \item{setMax}{If T then all variances below the max variance in the
    ordered distribution of variances are set to the maximum
    variance. If F then variances are left as is (recommended)}
 \item{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.}
 \item{df}{df stands for degrees of freedom. It is used in 
 	   smooth.spline function to interpolate the variances
	   of all genes. Default value is 10.}
}
 
\value{
  Returns object of class baseOlig, comprising a data frame with 2 columns: A
  and var M. The A column contains the median values of each gene 
  and the M columns contains the corresponding variance.  Number of 
  rows of the data-frame is same as that of the number of genes.
}

\author{ Carl Murie \email{carl.murie@mcgill.ca},
         Nitin Jain \email{nitin.jain@pfizer.com}}

\references{
	J.K. Lee and M.O.Connell(2003). \emph{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) \emph{Local pooled error test for identifying
      differentially expressed genes with a small number of replicated microarrays}, Bioinformatics, 1945-1951.

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

}


\seealso{
  \code{\link{lpeAdj}}
}

\examples{

  # Loading the library and the data
  library(LPEadj)
  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[1:1000,2:7] <- preprocess(Ley[1:1000,2:7],data.type="MAS5")
  # Finding the baseline distribution of subset of the data
  # condition one (3 replicates)
  var.1 <- adjBaseOlig.error.step1(Ley[1:1000,2:4], setMax=FALSE, q=0.01)
  dim(var.1)
  # Returns a matrix of 1000 by 2 (A,M) format
}
\keyword{methods} % from KEYWORDS.db