list.siggenes

object

a numeric value specifying the threshold $Delta$
      in the SAM or EBAM analysis. Note that the meaning of $Delta$
      differs between SAM and EBAM: In SAM, it is a strictly positive value, whereas
      in EBAM it is a probability.

delta

a character string naming a file in which the output is stored.
     If <code>""</code>, the significant genes will be shown in the console.

file

a character vector containing the names of the genes. Needs
     only to be specified, if the gene names were not specified in <code>sam</code> or
     <code>ebam</code>, respectively.

gene.names

if <code>TRUE</code>, the gene names will be ordered by their 
     "significance".

order

a character string specifying the heading of the gene list. By
     default, the header specifies the type of analysis and the used value of
     $Delta$. To avoid a header, set <code>text = ""</code>.

text

If <code>TRUE</code>, the output will be appended to <code>file</code>. If
     <code>FALSE</code>, any existing file having the name <code>file</code> will be destroyed.

append


  Lists the genes called differentially expressed by the SAM or the EBAM analysis for
  a specified value of the threshold $Delta$.


Identification of differentially expressed genes and
estimation of the False Discovery Rate (FDR) using both the
Significance Analysis of Microarrays (SAM) and the Empirical
Bayes Analyses of Microarrays (EBAM).

Holger Schwender

siggenes

Multiple testing using SAM and Efron's empirical Bayes
approaches

list.siggenes function

a numeric value specifying the threshold $\Delta$
      in the SAM or EBAM analysis. Note that the meaning of $\Delta$
      differs between SAM and EBAM: In SAM, it is a strictly positive value, whereas
      in EBAM it is a probability.

a character string naming a file in which the output is stored.
     If <code>""</code>, the significant genes will be shown in the console.

a character vector containing the names of the genes. Needs
     only to be specified, if the gene names were not specified in <code>sam</code> or
     <code>ebam</code>, respectively.

if <code>TRUE</code>, the gene names will be ordered by their 
     "significance".

a character string specifying the heading of the gene list. By
     default, the header specifies the type of analysis and the used value of
     $\Delta$. To avoid a header, set <code>text = ""</code>.

If <code>TRUE</code>, the output will be appended to <code>file</code>. If
     <code>FALSE</code>, any existing file having the name <code>file</code> will be destroyed.

Lists the genes called differentially expressed by the SAM or the EBAM analysis for
  a specified value of the threshold $\Delta$.

list.siggenes: List of the significant genes

Description

Usage

Arguments

Value

See Also