getNI_Eset-methods: Method to generate an ExpressionSet of non-informative genes
In farms: FARMS - Factor Analysis for Robust Microarray Summarization

Description Usage Arguments Value Methods See Also Examples

This function generates an instance of exprSet-class, that contains only non-informative probe sets.

1 2	## S4 method for signature 'INI_Calls' getNI_Eset(object)

object

An instance of INI_Calls-class.

exprSet-class

signature(object = "INI_Calls"): An instance of INI_Calls-class.

expFarms, qFarms,lFarms,INIcalls,summary

data(testAffyBatch)
eset <- expFarms(testAffyBatch, bgcorrect.method = "none", pmcorrect.method = "pmonly", normalize.method = "constant") 
INIs <- INIcalls(eset)  # apply I/NI calls
summary(INIs)
plot(INIs) # draws a density plot of I/NI-calls
I_data <- getI_Eset(INIs) # affybatch containing only informative probe sets
NI_data <- getNI_Eset(INIs) # affybatch containing only non-informative probe sets
I_probes <- getI_ProbeSets(INIs) # vector containing only informative probe sets names
NI_probes <- getNI_ProbeSets(INIs) # vector containing only  non-informative probe sets names

Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MASS
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Citation: S. Hochreiter et al.,
A new summarization method for affymetrix probe level data,
Bioinformatics, 22, 8, 943-949, 2006

Citation: W. Talloen et al.,
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,
Bioinformatics, 23, 21, 2897-2902, 2007
BibTex: enter 'toBibtex(citation("farms"))'

Homepage: http://www.bioinf.jku.at/software/farms/farms.html

FARMS Package Version 1.28.0


Changes in FARMS:
For all changes previous to 1.3.0, see the farms vignette.
Version 1.3.0: Added I/NI-calls for filtering
               Adjusted Hyperparameters for alternative CDFs,
               probes set standardized, weighted mean
               Works now with R >= 2.8 and Bioconductor 2.3,
               Changed termination criterion, initialization values,
               factors and loadings scaled, added argument robust
               Update for R-2.11
               Updated I/NI-Call for Laplace-FARMS version,
               Maximum likelihood correlation structure given
               non-negative constraints
Version 1.4.0: Default centering changed to median
Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't connect to server'
background correction: none 
normalization: constant 
PM/MM correction : pmonly 
expression values: farms 
background correcting...done.
normalizing...done.
2 ids to be processed
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Summary 
Informative probe sets      : 0% 
Non-Informative probe sets  : 100%