\HeaderA{heeboQuality}{Diagnostics plots designed for HEEBO set controls}{heeboQuality}
\keyword{dynamic}{heeboQuality}
\begin{Description}\relax
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.
\end{Description}
\begin{Usage}
\begin{verbatim}
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, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fnames}] A "character" string naming the input files.
\item[\code{path}] A "character" string representing the data directory.  By
default this is set to the current working directory (".").
\item[\code{galfile}] A "character" string naming the file descrining the
layout of the array. If missing, meeboQuality will read the layour
from the gpr file.
\item[\code{source}] A "character" string specifing the image analysis program
which produced the output files. See ?read.maimages in package limma
for more details.
\item[\code{other.columns}] See ?read.maimages in package limma for more
details.
\item[\code{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.
\item[\code{controlId}] Character string. Name of the column of the gpr
file (or gal file) used to define controls.
\item[\code{DOPING}] Logical. If 'TRUE', doping controls quality plots are
generated.
\item[\code{heeboSetQC}] Logical. If 'TRUE', mismatch and tiling controls
quality plots are generated.
\item[\code{SpotTypeFile}] A "character" string representing the name of the
file containing spot type description for the array.
\item[\code{SpikeTypeFile}] A "character" string representing the name of the
file containing doping control information. See HTML description for
more details.
\item[\code{cy3col}] A "character" string representing the name of the column
of the SpiketypeFile containing the quantity of each control spiked
in the Cy3 channel.
\item[\code{cy5col}] A "character" string representing the name of the column
of the SpiketypeFile containing the quantity of each control spiked
in the Cy5 channel.
\item[\code{id}] A "character" string describing which column of the MEEBO
annotation should be used to retrieve replicated oligos,
e.g. "SeqID".
\item[\code{namecol}] A "character" string describing which column of the
SpiketypeFile should be used in the legend.
\item[\code{annot}] A "character" string describing which R object should be
used to look-up probes annotations. By default, it will be set to
HEEBOset.
\item[\code{bgMethod}] Character string specifying which background
correction method to use. See ?backgroundCorrect in package limma
for more details.
\item[\code{normMethod}] Character string specifying which normalization
method should be used. See ?normalizeWithinArrays in package limma
for more details.
\item[\code{diagnosticPlot}] Logical. If 'TRUE', a quality diagnostic plot
will be generated.
\item[\code{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.
\item[\code{resdir}] A "character" string representing the directory where
the results will be saved. By default, this is set to the current
working directory ("."). 
\item[\code{dev}] A "character" string naming the graphics device. This will
take arguments "png", "jpeg" and "ps" only. By default, dev is set
to "png".
\item[\code{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.
\item[\code{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{...}] Additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
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.
\end{Details}
\begin{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.
\end{Value}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{heeboQualityPlots}{heeboQualityPlots}}, \code{\LinkA{gpQuality}{gpQuality}},
\code{\LinkA{meeboQuality}{meeboQuality}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
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)
}
\end{ExampleCode}
\end{Examples}

