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.’ Blood102, 2951–9.
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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'q()' to quit R.
> library(mdqc)
Loading required package: cluster
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mdqc/allQC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: allQC
> ### Title: QC report for MLL.B
> ### Aliases: allQC
> ### Keywords: datasets
>
> ### ** Examples
>
> data(allQC)
>
>
>
>
>
> dev.off()
null device
1
>