marrayTools {marray} | R Documentation

## Wrapper function

### Description

This functions will produce a directory of diagnostic plots, quality measures and normalization.

### Usage

    spotTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE,
                     quality = TRUE, fill = TURE, raw = FALSE, echo =
                     TRUE, ...)

    gpTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TRUE, raw = FALSE, echo = TRUE, ...)

### Arguments

`fnames` | a vector of character strings containing the file names of each spot quantification data file. These typically end in `.spot` for the software `Spot` or `.gpr` for the software `GenePix`.
`path` | a character string representing the data directory. By default this is set to the current working directory ("."). In the case where `fnames` contains the full path name, path should be set to NULL.
`galfile` | a character string representing the Gal file.
`bg` | logical: if 'TRUE', background correction is performed before normalization
`plot` | logical: if 'TRUE', maDiagnPlots is call to generate basic diagnostic plot per array.
`quality` | logical: if 'TRUE', maQuality is call to calculate basic quality measures.
`fill` | logical: if `TRUE', `scan' will implicitly add empty fields to any lines with fewer fields than implied by `what'.
`raw` | logical: if 'TRUE', the microarray object class of 'marrayRaw' is return rather than 'marrayNorm'.
`echo` | logical: if 'TRUE' (default), run-time information of the array currently being process is printed.
`...` | further arguments to `scan` or `maNorm`.

### Value

Jpeg files of diagnostic plots, excel files of quality measures, tab delimited files of normalized log-ratios and log-intensities values are saved to disk. In addition, an object of class `marrayRaw` or `marrayNorm` is return.

### Author(s)

Yee Hwa (Jean) Yang

### See Also

`read.marrayRaw`

### Examples

     data(swirl)
     datadir <- system.file("swirldata", package="marray")

    ## normdata <- spotTools(path=datadir, quality=FALSE)

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