normalize_pools

Normalize nanostring gene expression using common pools between two CodeSets.

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

normalize_pools function

<dl><dt>x</dt>
<dd>target data</dd>
<dt>x_pools</dt>
<dd>target pool samples</dd>
<dt>ref_pools</dt>
<dd>reference pool samples</dd>
<dt>p</dt>
<dd>number of pool sample sets. Defaults to 3.</dd>
<dt>weigh</dt>
<dd>logical; if <code>TRUE</code>, the average expression in <code>x_pools</code> is
reweighed by the distribution of the <code>p</code> pool sample sets in <code>ref_pools</code>.</dd></dl>

Arguments

Author

Normalize data using common pools — normalize_pools

<dl>

<dt>x</dt>
<dd>target data</dd>


<dt>x_pools</dt>
<dd>target pool samples</dd>


<dt>ref_pools</dt>
<dd>reference pool samples</dd>


<dt>p</dt>
<dd>number of pool sample sets. Defaults to 3.</dd>


<dt>weigh</dt>
<dd>logical; if <code>TRUE</code>, the average expression in <code>x_pools</code> is
reweighed by the distribution of the <code>p</code> pool sample sets in <code>ref_pools</code>.</dd>

</dl>

normalize_pools: Normalize data using common pools

Description

Usage

Value

Arguments

Author

Details