plot.qc.stats: Plots a QCStats object
In simpleaffy: Very simple high level analysis of Affymetrix data

Description Arguments Details Usage Author(s) See Also Examples

Generates a visual summary of the various QC statistics recommended by Affymetrix in their 'Data Analysis Fundamentals' handbook.

`x`	A `QCStats` object
`fc.line.col`	The colour to mark fold change lines with
`sf.ok.region`	The colour to mark the region in which scale factors lie within appropriate bounds
`chip.label.col`	The colour to label the chips with
`sf.thresh`	Scale factors must be within this fold-range
`gdh.thresh`	Gapdh ratios must be within this range
`ba.thresh`	beta actin must be within this range
`present.thresh`	The percentage of genes called present must lie within this range
`bg.thresh`	Array backgrounds must lie within this range
`label`	What to call the chips
`main`	The title for the plot
`usemid`	If true use 3'/M ratios for the GAPDH and beta actin probes
`cex`	Value to scale character size by (e.g. 0.5 means that the text should be plotted half size)
`...`	Other parameters to pass through to `plot`

A lot of information is presented in this one figure. By default, each array is represented by a seperate line in the figure. The central vertical line corresponds to 0 fold change, the dotted lines on either side correspond to 3 fold up and down regulation. The blue bar represents the region in which all arrays have scale factors within, by default, three-fold of each other. Its position is found by calculating the mean scale factor for all chips and placing the center of the region such that the borders are -1.5 fold up or down from the mean value.

Each array is plotted as a line from the 0-fold line to the point that corresponds to its scale factor. If the ends of all of the lines are in the blue region, their scale-factors are compatible. The lines are coloured blue if OK, red if not.

The figure also shows GAPDH and beta-actin 3'/5' ratios. These are represented as a pair of points for each chip. Affy state that beta actin should be within 3, gapdh around 1. Any that fall outside these thresholds (1.25 for gapdh) are coloured red; the rest are blue.

Written along the left hand side of the figure are the number of genes called present on each array and the average background. These will vary according to the samples being processed, and Affy's QC suggests simply that they should be similar. If any chips have significantly different values this is flagged in red, otherwise the numbers are displayed in blue. By default, 'significant' means that %-present are within 10% of each other; background intensity, 20 units. These last numbers are somewhat arbitrary and may need some tweaking to find values that suit the samples you're dealing with, and the overall nature of your setup.

Finally, if BioB is not present on a chip, this will be flagged by printing 'BioB' in red.

In short, everything in the figure should be blue - red highlights a problem!

plot.qc.stats(x, fc.line.col = "black", sf.ok.region = "light blue", chip.label.col = "black", sf.thresh = 3, gdh.thresh = 1.25, ba.thresh = 3, present.thresh = 10, bg.thresh = 20, label = NULL,title="QC Stats",spread=c(-8,8),usemid=F,type="l",cex=1, ...)

Crispin J Miller

qc

1 2	data(qcs) plot(qcs)

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
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    Vignettes contain introductory material; view with
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    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affy
Loading required package: genefilter
Loading required package: gcrma
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