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

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This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.

Author
Nitin Jain <emailnitinjain@gmail.com>, Michael O'Connell <michaelo@warath.com>, Jae K. Lee <jaeklee@virginia.edu>. Includes R source code contributed by HyungJun Cho <hcho@virginia.edu>
Date of publication
None
Maintainer
Nitin Jain <emailnitinjain@gmail.com>
License
LGPL
Version
1.48.0
URLs

View on Bioconductor

Man pages

am.trans
Transform replicated arrays into (A,M) format
baseOlig.error
Evaluates LPE variance function of M for quantiles of A...
baseOlig.error.step1
Evaluates LPE variance function of M for quantiles of A...
baseOlig.error.step2
Evaluates LPE variance function of M for quantiles of A...
fdr.adjust
FDR adjustment procedures
fixbounds.predict.smooth.spline
Makes the predicted variance non negative
iqr
Inter-quartile range
Ley
Gene Expression Data from Mouse Immune response study, (2002)
lowess.normalize
lowess normalization of the data (based on M vs A graph)
lpe
Evaluates local pooled error significance test
mt.rawp2adjp
Adjusted p-values for simple multiple testing procedures
n.genes.adaptive.int
Calcuates the number of genes in various intervals...
permute
Calculating all possible permutations of a vector
preprocess
Preprocessing the data (IQR normalization, thresholding, log-...
quan.norm
Finding quartile range
quartile.normalize
Normalization based on quartile range
resamp.adj
Resampling based fdr adjustment

Files in this package

LPE/DESCRIPTION
LPE/NAMESPACE
LPE/NEWS
LPE/R
LPE/R/am.trans.R
LPE/R/baseOlig.error.R
LPE/R/baseOlig.error.step1.R
LPE/R/baseOlig.error.step2.R
LPE/R/fdr.adjust.R
LPE/R/fixbounds.predict.smooth.spline.R
LPE/R/iqr.R
LPE/R/lowess.normalize.R
LPE/R/lpe.R
LPE/R/mt.rawp2adjp.R
LPE/R/n.genes.adaptive.int.R
LPE/R/permute.R
LPE/R/preprocess.R
LPE/R/quan.norm.R
LPE/R/quartile.normalize.R
LPE/R/resamp.adj.R
LPE/TODO
LPE/build
LPE/build/vignette.rds
LPE/data
LPE/data/Ley.RData
LPE/inst
LPE/inst/doc
LPE/inst/doc/LPE.R
LPE/inst/doc/LPE.Rnw
LPE/inst/doc/LPE.pdf
LPE/man
LPE/man/Ley.Rd
LPE/man/am.trans.Rd
LPE/man/baseOlig.error.Rd
LPE/man/baseOlig.error.step1.Rd
LPE/man/baseOlig.error.step2.Rd
LPE/man/fdr.adjust.Rd
LPE/man/fixbounds.predict.smooth.spline.Rd
LPE/man/iqr.Rd
LPE/man/lowess.normalize.Rd
LPE/man/lpe.Rd
LPE/man/mt.rawp2adjp.Rd
LPE/man/n.genes.adaptive.int.Rd
LPE/man/permute.Rd
LPE/man/preprocess.Rd
LPE/man/quan.norm.Rd
LPE/man/quartile.normalize.Rd
LPE/man/resamp.adj.Rd
LPE/vignettes
LPE/vignettes/LPE.Rnw
LPE/vignettes/isorot.sty