ffpe (version 1.16.0)

ffpe-package: Quality assessment and control for FFPE microarray expression data

Description

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).

Details

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.

References

under review

Examples

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"))