siggenes2excel {siggenes} | R Documentation

## CSV file of a SAM or an EBAM object

### Description

Generates a csv file for either a SAM or an EBAM object for the use in Excel. This csv file can contain general information as the number of differentially expressed genes and the estimated FDR, and gene-specific information on the differentially expressed genes.

### Usage

     sam2excel(object, delta, file, excel.version=1, n.digits = 3, what = "both",
            entrez = FALSE, chip = "", quote = FALSE)

     ebam2excel(object, delta, file, excel.version=1, n.digits = 4, what = "both",
            entrez = FALSE, chip = "", quote = FALSE)

### Arguments

`object` | either a SAM or an EBAM object.
`delta` | a numerical value specifying the Delta value.
`file` | character string naming the file in which the output should be stored. Must have the suffix ".csv".
`excel.version` | either `1` or `2`. If `excel.version=1` (default) a csv file for the use in an Excel version with American standard settings (`sep=","` and `dec="."`) will be generated. If `excel.version=2` a csv file for the European standard setting (`sep=";"` and `dec=","`) will be generated.
`n.digits` | integer specifying the number of decimal places used in the output.
`what` | either `"both"`, `"stats"` or `"genes"`. If `"stats"` general information will be shown. If `"genes"` gene-specific information will be given. If `"both"` both general and gene-specific information will be shown.
`entrez` | logical indicating if both the Entrez links and the symbols of the genes will be added to the output.
`chip` | character string naming the chip type used in this analysis. Must be specified as in the meta-data section of Bioconductor (e.g., `"hgu133a"` for the Affymetrix HG-U133A chip). Only needed if `ll = TRUE`. If the argument `data` in `sam(data, cl, ...)` has been specified by an `ExpressionSet` object `chip` need not to be specified.
`quote` | logical indicating if character strings and factors should be surrounded by double quotes. For details see `write.table`.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### See Also

`sam`, `sam2html`, `ebam`, `ebam2html`

[Package siggenes version 1.64.0 Index]