heeboQuality {arrayQuality} | R Documentation

## Diagnostics plots designed for HEEBO set controls

### Description

This component generates several exploratory plots customized to the various types of controls provided in the HEEBO set. All results are saved as an image. Tested on GenePix format only (06-29-2006). For more details about the plots, please refer to the HTML description.

### Usage

    heeboQuality(fnames = NULL, path = ".", galfile = NULL, source
    ="genepix.median", other.columns =
    c("Flags"), controlMatrix=HeeboSpotTypes,controlId = c("ID", "Name"),
    DOPING = TRUE, heeboSetQC = TRUE, SpotTypeFile = NULL, SpikeTypeFile =
    NULL, cy3col = "Cy3_ng", cy5col = "Cy5_ng", id = "SeqID", namecol =
    c("Symbol", "Name"), annot = NULL, bgMethod = "none", normMethod = "p",
    diagnosticPlot = TRUE, output = TRUE, resdir = ".", dev = "png",
    organism = "Hs", DEBUG = FALSE, ...)

### Arguments

`fnames` | A "character" string naming the input files.
`path` | A "character" string representing the data directory. By default this is set to the current working directory (".").
`galfile` | A "character" string naming the file descrining the layout of the array. If missing, meeboQuality will read the layour from the gpr file.
`source` | A "character" string specifing the image analysis program which produced the output files. See ?read.maimages in package limma for more details.
`other.columns` | See ?read.maimages in package limma for more details.
`controlMatrix` | A character matrix of n by 2 or more columns. One column should contain a few regular expression of spotted probe sequences and another column should contain the corresponding control status. By default, controlMatrix is set to HeeboSpotTypes.
`controlId` | Character string. Name of the column of the gpr file (or gal file) used to define controls.
`DOPING` | Logical. If 'TRUE', doping controls quality plots are generated.
`heeboSetQC` | Logical. If 'TRUE', mismatch and tiling controls quality plots are generated.
`SpotTypeFile` | A "character" string representing the name of the file containing spot type description for the array.
`SpikeTypeFile` | A "character" string representing the name of the file containing doping control information. See HTML description for more details.
`cy3col` | A "character" string representing the name of the column of the SpiketypeFile containing the quantity of each control spiked in the Cy3 channel.
`cy5col` | A "character" string representing the name of the column of the SpiketypeFile containing the quantity of each control spiked in the Cy5 channel.
`id` | A "character" string describing which column of the MEEBO annotation should be used to retrieve replicated oligos, e.g. "SeqID".
`namecol` | A "character" string describing which column of the SpiketypeFile should be used in the legend.
`annot` | A "character" string describing which R object should be used to look-up probes annotations. By default, it will be set to HEEBOset.
`bgMethod` | Character string specifying which background correction method to use. See ?backgroundCorrect in package limma for more details.
`normMethod` | Character string specifying which normalization method should be used. See ?normalizeWithinArrays in package limma for more details.
`diagnosticPlot` | Logical. If 'TRUE', a quality diagnostic plot will be generated.
`output` | Logical. If 'TRUE', normalized M values and A values corresponding to the input GenePix files and additionnal quality measures are printed to a file.
`resdir` | A "character" string representing the directory where the results will be saved. By default, this is set to the current working directory (".").
`dev` | A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only. By default, dev is set to "png".
`organism` | A "character" string naming the organism genome printed on the array, either "Mm" or "Hs". By default, organism is set to "Hs". It is used to retrieve the corresponding Oligo set annotations.
`DEBUG` | If 'TRUE', debug statements are printed.
`...` | Additional arguments

### Details

heeboQuality returns 3 types of quality control plots, specifically designed for the various controls offered by the HEEBO set. To assess the global performance of an hybridization, users can generate a diagnostic plot summarizing several graphs and statictics by setting'diagnosticPlot=TRUE'. Then, the performance of the HEEBO set can beanalyzed by looking specifically at the mismatch and the tiling controls ('heeboSetQC=TRUE').

Finally, we are also providing several exploratory tools to assess the performance of the doping-controls ('DOPING=TRUE');these plots should be used only if a spike-in mixture was added to the hybridization solution.

### Value

heeboquality will produce several graphs, saved in an image file format. Please refer to the HTML description for more details. The function will also return the MAList object describing your tested slides.

### Author(s)

Agnes Paquet

### See Also

`heeboQualityPlots`, `gpQuality`, `meeboQuality`

### Examples

    if (interactive())
    {
    require(HEEBOdata)
    datadir <- system.file("Heebo", package="HEEBOdata")
    MA <-
    heeboQuality(fnames="63421.gpr",galfile="hoc.gal",path=datadir,SpikeTypeFile="DCV2.0June06.txt",cy5col="Cy5_ng",cy3col="Cy3_ng",diagnosticPlot=TRUE,
    DOPING=TRUE, heeboSetQC=TRUE, namecol="Name", resdir="HeeboQC", DEBUG=TRUE)
    }

[Package arrayQuality version 1.12.0 Index]