preprocess: Preprocessing the data (IQR normalization, thresholding, log-...

In LPE: Methods for analyzing microarray data using Local Pooled Error (LPE) method

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 does lowess normalization

Usage

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

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. If LOWESS normalization parameter is set as TRUE, then lowess normalization is performed.

Author(s)

Nitin Jain [e-mail]

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

  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,]
 

Example output

[1] 12488     7
               ID   c1   c2   c3     t1     t2     t3
1  AFFX-MurIL2_at 16.0 14.1 19.3 2782.7 2861.3 2540.2
2 AFFX-MurIL10_at 22.7  6.9 28.2   18.6   12.7    7.5
3  AFFX-MurIL4_at 33.9 17.1 23.9   24.9   25.2   24.9
               ID       c1       c2       c3        t1        t2        t3
1  AFFX-MurIL2_at 4.304733 4.386399 4.791980 11.713336 11.723762 11.557357
2 AFFX-MurIL10_at 4.809354 3.374603 5.308619  5.306709  4.601048  3.958138
3  AFFX-MurIL4_at 5.387947 4.615203 5.060382  5.659498  5.522553  5.528363

LPE documentation built on Nov. 8, 2020, 5:25 p.m.