TCGAanalyze_Preprocessing

of gene expression of class RangedSummarizedExperiment from TCGAprepare

object

is a threshold to filter samples according their spearman correlation in
samples by samples. default cor.cut is 0

cor.cut

filename

width

height


TCGAanalyze_Preprocessing perform Array Array Intensity correlation (AAIC).
It defines a square symmetric matrix of pearson correlation among samples.
According this matrix and boxplot of correlation samples by samples it is possible
to find samples with low correlation that can be identified as possible outliers.


The aim of TCGAbiolinks is : i) facilitate the TCGA open-access
data retrieval, ii) prepare the data using the appropriate pre-processing
strategies, iii) provide the means to carry out different standard analyses
and iv) allow the user to download a specific version of the data and thus
to easily reproduce earlier research results. In more detail, the package
provides multiple methods for analysis (e.g., differential expression analysis,
identifying differentially methylated regions) and methods for visualization
(e.g., survival plots, volcano plots, starburst plots) in order to easily
develop complete analysis pipelines.

Antonio Colaprico

TCGAbiolinks

TCGAbiolinks: An R/Bioconductor package for integrative analysis with
TCGA data

TCGAanalyze_Preprocessing function

TCGAanalyze_Preprocessing perform Array Array Intensity correlation (AAIC).
It defines a square symmetric matrix of pearson correlation among samples.
According this matrix and boxplot of correlation samples by samples it is possible
to find samples with low correlation that can be identified as possible outliers.

TCGAanalyze_Preprocessing: Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier

Description

Usage

Arguments

Value

Examples