ArrayOutliers {arrayMvout} | R Documentation |
Multivariate outlier detection based on PCA of QA statistics
ArrayOutliers (data, alpha, alphaSeq = c(0.01, 0.05, 0.1), ... ) # qcOutput = NULL, plmOutput = NULL, degOutput = NULL, prscale = TRUE, # pc2use = 1:3)
data |
an (affy) AffyBatch instance with at least 11 samples |
alpha |
false positive rate for outlier detection, adjusting for multiple comparisons according to Caroni and Prescott's adaptation of Rosner (1983); full report based on this choice of alpha |
alphaSeq |
vector of alpha candidates to be quickly tried for short report |
... |
additional parameters, see below |
Additional parameters may be supplied
Data elements afxsubDEG, afxsubQC, s12cDEG, s12cQC are precomputed RNA degradation and simpleaffy qc() results; s12c is an AffyBatch with digital contamination of some samples.
Data elements maqcQA and itnQA are affymetrix QC statistics on large collections of arrays. Data element ilmQA is a derived from a LumiBatch of the Illumina-submitted MAQC raw data, 19 arrays. (Conveyed by Leming Shi, personal communication). Data element spikQA is a 12x9 matrix of QA parameters obtained for 12 arrays from U133A spikein dataset, with first 2 arrays digitally contaminated as described in Asare et al.
Data element fig3map gives the indices of the points labeled A-H in Figure 3 of the manuscript by Asare et al. associated with this package.
an instance of arrOutStruct class, a list with a partition of samples into two data frames (inl and outl) with QA summary statistics
Z. Gao et al.
library(simpleaffy) setQCEnvironment("hgu133acdf") # no CDF corresponding to tag array if ( require("mvoutData") ) { data(s12c) data(s12cQC) data(s12cDEG) library(affyPLM) s12cPset = fitPLM(s12c) ao = ArrayOutliers(s12c, alpha=0.05, qcOut=s12cQC, plmOut=s12cPset, degOut=s12cDEG) ao } if (require("lumiBarnes")) { library(lumiBarnes) data(lumiBarnes) ArrayOutliers(lumiBarnes, alpha=0.05) lb2 = lumiBarnes exprs(lb2)[1:20000,1:2] = 10000*exprs(lb2)[1:20000,1:2] ArrayOutliers(lb2, alpha=0.05) } data(maqcQA) # affy ArrayOutliers(maqcQA[,-c(1:2)], alpha=.05) ArrayOutliers(maqcQA[,-c(1:2)], alpha=.01) data(ilmQA) # illumina ArrayOutliers(data.frame(ilmQA), alpha=.01) data(itnQA) # 507 arrays from ITN ArrayOutliers(itnQA, alpha=.01)