allQC {mdqc} | R Documentation |
A subset of arrays from a large acute lymphoblastic leukemia (ALL) study
data(allQC)
A data frame with 20 observations on the following 11 variables.
Scale Factor
Percent Present
Average Background
Minimum Background
Maximum Background
BioB
BioC
BioD
CreX
AFFX-HSAC07/X00351.3'/5'
AFFX-HUMGAPDH/M33197.3'/5'
Contains the QC report obtained using Bioconductor's simpleaffy package for a subset of arrays from a large acute lymphoblastic leukemia (ALL) study (Ross et al., 2004). The QC report in allQC has been generated using the following R commands:
library("affy") ## Get the raw data (see help("MLL.B") for further details) library("ALLMLL") data(MLL.B) ## Generate the QC metrics library("simpleaffy") data.all <- MLL.B[,1:20] all.qc <- qc(data.all) ## Select relevant information allQC <- cbind(sfs(all.qc),percent.present(all.qc)/100, avbg(all.qc),minbg(all.qc),maxbg(all.qc), spikeInProbes(all.qc),ratios(all.qc)[,c(1,3)]) ## Specify row and column names colnames(allQC) <- c("Scale Factor","Percent Present", "Average Background", "Minimum Background", "Maximum Background", "BioB", "BioC", "BioD", "CreX", "AFFX-HSAC07/X00351.3'/5'", "AFFX-HUMGAPDH/M33197.3'/5'") rownames(allQC) <- 1:20Versions 1.16.0 of ‘affy’, 1.2.2 of ‘ALLMLL’, and 2.14.05 of ‘simpleaffy’ was used. Part of this dataset has been also studied by Bolstad et al. (2005) and Brettschneider et al. (2007).
Ross, M. E. and Zhou, X. and Song, G. and Shurtleff, S. A. and Girtman, K. and Williams, W. K. and Liu, H. and Mahfouz, R. and Raimondi, S. C. and Lenny, N. and Patel, A. and Downing, J. R. (2003) ‘Classification of pediatric acute lymphoblastic leukemia by gene expression profiling.’ Blood 102, 2951–9.
All CEL files are freely available in http://www.stjuderesearch.org/data/ALL3/rawFiles.html.
Bolstad, B. M. and Collin, F. and Brettschneider, J. and Simpson, K. and Cope, L. and Irizarry R. A. and Speed T. P. (2005) ‘Quality assessment of Affymetrix GeneChip data.’ In Gentleman, R. and Carey, C. J. and Huber, W. and Irizarry, R. A. and Dudoit, S. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer.
Brettschneider, J. and Collin, F. and Bolstad, B. M. and Speed, T. P. (2007) ‘Quality assessment for short oligonucleotide arrays’. Forthcoming in Technometrics (with Discussion).
data(allQC)