ffpe-package {ffpe} | R Documentation |
Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).
Package: | ffpe |
Type: | Package |
Version: | 1.0.0 |
Date: | 2011-11-17 |
License: | GPL (>=2) |
LazyLoad: | yes |
biocViews: | Microarray, GeneExpression, QualityControl, Bioinformatics |
Quality control of FFPE expression data for Illumina and Affymetrix microarrays. The function sampleQC identifies low-quality expression data, using IQR or any other surrogate quality measure for expression data. sortedIqrPlot provides a simplified, sorted boxplot of raw expression intensities as a quality summary for the experiment, suitable for large sample sizes and multiple batches.
Levi Waldron
Maintainer: Levi Waldron <lwaldron@hsph.harvard.edu>
under review
library(ffpeExampleData) data(lumibatch.GSE17565) QC <- sampleQC(lumibatch.GSE17565,xaxis="index",cor.to="pseudochip",QCmeasure="IQR") ##sort samples QCvsRNA <- data.frame(inputRNA.ng=lumibatch.GSE17565$inputRNA.ng,rejectQC=QC$rejectQC) QCvsRNA <- QCvsRNA[order(QCvsRNA$rejectQC,-QCvsRNA$inputRNA.ng),] ##QC rejects samples with lowest input RNA concentration\n par(mgp=c(4,2,0)) dotchart(log10(QCvsRNA$inputRNA.ng), QCvsRNA$rejectQC, xlab="log10(RNA conc. in ng)", ylab="rejected?", col=ifelse(QCvsRNA$rejectQC,"red","black"))