myCounts-class

myCounts


This is the main class which contains the information needed to do the different analyses.


classes

Analysis of RNA-seq expression data or other similar kind
of data. Exploratory plots to evualuate saturation, count
distribution, expression per chromosome, type of detected
features, features length, etc. Differential expression between
two experimental conditions with no parametric assumptions.

Sonia Tarazona

NOISeq

Exploratory analysis and differential expression for RNA-seq
data

myCounts function

Class <code>eSet</code> (package 'Biobase').

Extends

This object will contain the expression data and further information needed to do the exploratory analysis or the normalization such as the length, GC content, biotypes, chromosomes and positions for each feature. Internally, the data is stored as follows: As <code>myCounts</code> derives from <code>eSet</code>, we have used the slot <code>assayData</code> to store all the expression data, <code>phenoData</code> to store the factors with the conditions, <code>featureData</code> which will contain the variables <code>Length</code>, <code>GCcontent</code>, <code>Biotype</code>, <code>Chromosome</code>, Start Position, <code>End Position</code> for each feature. It has been used the slot <code>experimentData</code> derived from <code>MIAME-class</code> which will contain the type of replicates (biological replicates, technical replicates or no replicates at all).

myCounts: Class myCounts

Description

Arguments

Extends

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