Sample correlation and heatmap - Githubissues

mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.

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Sample correlation and heatmap #1

Closed hcorrada closed 9 years ago

hcorrada commented 9 years ago

Added a section on sample correlation plots:

a pairwise correlation heatmap
a QA plot to identify possible outlier samples

Also added a slight modification of the heatmap.2 function that has some niceties:

uses a pleasant color palette by default
can take matrices for 'RowSideColors' and 'ColSideColors' to annotate more than one variable

Slightly modified the sample heatmap section:

do heatmap on log2CPM values
use new heatmap function