affySpikeIn

affySpikeIn.L

affySpikeIn.gnames

spikedgene


The spike-in experiment represents a portion of the data used by Affymetrix
to develop their MAS 5.0 preprocessing algorithm.  Here we utilize the
RMA (Irizarry et. al) probe level summaries.  The data features 14 
human genes spiked-in at a series of 14 known concentrations 
($0, 2^{-2}, 2^{-1}, \ldots, 2^{10}$ pM) according to 
a Latin square design among 12612 null genes.  The data matrix
<code>affySpikeIn</code> represents the two array groups among the 14 array
groups that contain 12 replicates. Further details are available 
at <a href="http://www.affymetrix.com/analysis/download_center2.affx">http://www.affymetrix.com/analysis/download_center2.affx</a>. 

datasets

This library contains functions that calculate various
statistics of differential expression for microarray data,
including t statistics, fold change, F statistics, SAM,
moderated t and F statistics and B statistics. It also
implements a new methodology called DEDS (Differential
Expression via Distance Summary), which selects differentially
expressed genes by integrating and summarizing a set of
statistics using a weighted distance approach.

Yuanyuan Xiao

DEDS

Differential Expression via Distance Summary for Microarray Data

affySpikeIn function

The spike-in experiment represents a portion of the data used by Affymetrix
to develop their MAS 5.0 preprocessing algorithm.  Here we utilize the
RMA (Irizarry et. al) probe level summaries.  The data features 14 
human genes spiked-in at a series of 14 known concentrations 
($0, 2^{-2}, 2^{-1}, \ldots, 2^{10}$ pM) according to 
a Latin square design among 12612 null genes.  The data matrix
<code>affySpikeIn</code> represents the two array groups among the 14 array
groups that contain 12 replicates. Further details are available 
at <url>http://www.affymetrix.com/analysis/download_center2.affx</url>.

Gene expression dataset from Affymetrix Spike-in Experiments

matrix of gene expression levels measurements,
    rows correspond to genes (12626 genes) and columns to 24 samples.

numeric vector indicating the sample class, 12 (code 0)
    vs. 12 (code 1).

character vector containing the names of the
    12626 genes.

numeric vector given the location of the 14 spiked genes.

affySpikeIn: Gene expression dataset from Affymetrix Spike-in Experiments

Description

Usage

Arguments

Value

References