allQC: QC report for MLL.B

In mdqc: Mahalanobis Distance Quality Control for microarrays

Description

A subset of arrays from a large acute lymphoblastic leukemia (ALL) study

Usage

data(allQC)

Format

A data frame with 20 observations on the following 11 variables.

Scale Factor

a numeric vector

Percent Present

a numeric vector

Average Background

a numeric vector

Minimum Background

a numeric vector

Maximum Background

a numeric vector

BioB

a numeric vector

BioC

a numeric vector

BioD

a numeric vector

CreX

a numeric vector

AFFX-HSAC07/X00351.3'/5'

a numeric vector

AFFX-HUMGAPDH/M33197.3'/5'

a numeric vector

Details

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) <- 1:20
  

Versions 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).

Source

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.

References

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).

Examples

data(allQC)

mdqc documentation built on Nov. 8, 2020, 11 p.m.