HKnorm

Normalizes the gene expression of NanoString nCounter data to housekeeping
genes. This is done by subtracting the average log housekeeping gene
expression from the expression level of every gene in each sample.

Provides quality control (QC), normalization, and batch
effect correction operations for 'NanoString nCounter' data, Talhouk
et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are
used to determine which samples passed or failed QC. Gene expression
should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.

Derek Chiu

nanostringr

Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data

Aline Talhouk

Samuel Leung

HKnorm function

<dl><dt>raw</dt>
<dd>data frame of raw counts obtained from nCounter (rows represent
genes, columns represent samples). The first three columns must be labeled:
<code>c("Code.Class", "Name", "Accession")</code> and contain that information.</dd>
<dt>is.logged</dt>
<dd>logical; If <code>TRUE</code>, normalization has already been done on
log base 2 scale, no need log the data</dd>
<dt>corr</dt>
<dd>small correction to avoid error</dd></dl>

Arguments

Author

Normalization to Housekeeping Genes — HKnorm

<dl>

<dt>raw</dt>
<dd>data frame of raw counts obtained from nCounter (rows represent
genes, columns represent samples). The first three columns must be labeled:
<code>c("Code.Class", "Name", "Accession")</code> and contain that information.</dd>


<dt>is.logged</dt>
<dd>logical; If <code>TRUE</code>, normalization has already been done on
log base 2 scale, no need log the data</dd>


<dt>corr</dt>
<dd>small correction to avoid error</dd>

</dl>

HKnorm: Normalization to Housekeeping Genes

Description

Usage

Value

Arguments

Author

Examples