adjBaseOlig.error.step2 {LPEadj} | R Documentation

## Evaluates LPE variance function of M for quantiles of A within and experimental condition. It is based on the adaptive number of intervals.

### Description

Similar to adjBaseOlig.error.step1 function, except that now the number of bins are chosen adaptively instead of fixed 100.

### Usage

      adjBaseOlig.error.step2(y, baseOlig.error.step1.res, df=10, stats=median, setMax=FALSE, 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.
`baseOlig.error.step1.res` | It is the result obtained from adjBaseOlig.error.step1 function, in which number of bins are fixed=100
`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.
`stats` | It determines whether mean or median is to be used for the replicates
`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)
`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.

### Author(s)

Carl Murie carl.murie@mcgill.ca, Nitin Jain nitin.jain@pfizer.com

### 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

`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], q=0.01, df=10)
      dim(var.1)
      var.11 <- adjBaseOlig.error.step2(Ley[1:1000,2:4], var.1, df=10)
      # Returns a matrix of 1000 by 2 (A,M) format

[Package LPEadj version 1.4.0 Index]