Adds function for averaging replicates within a matrix
Script for subtyping cell line data sets
Added description for subtyping_celllines.r
Add CCLE subtyping
Merge branch 'master' of https://github.com/andreas-schlicker/crcsc
Adds GSE17536
loadMatrix only searches for duplicates if the first column is not
numeric.
Fixes bug in subtypingMatrix: If any name is NA, ignore the solution.
Subtype new TCGA data sets;
File with mapping of identifiers can be quoted
Apply additional mean-centering to the TCGA microarray set
Adds functionality to randomize features to run iNMF subtyping
Assigns confidence HIGH or LOW to each sample-subtype assignment. The
margin cut-off was selected based on subtyping randomized data sets.
Use subtyping results stored in Synapse:
- doesn't depend on local files
- makes provenance tracking easier
Fixes bug: need to add quotes for synapseQuery
Fixes bug: need quotes for synapseQuery
Fixes bug
Fixes bug: dataset has only one dimension
Merge branch 'master' of https://github.com/andreas-schlicker/crcsc.git
Changes apply to for-loop
Normalize public datasets using fRMA