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MeapNormalization

Prepares normalized data at probe level. It does PM-BayesBG background correction and collective quantile normalization. Processing is run in parallel using the R Message Passing Interface (Rmpi) library to enable faster execution.

It now supports Affymetrix GeneChip Exon 1.0 ST and Gene 1.0 ST arrays. This version is build on latest meap library (2.0.0) and Ensembl v70.

Version 2.0
Bundle microarray
Categories Meap
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires R ; libopenmpi-dev (DEB) ; openmpi-bin (DEB) ; meap (R-package) ; installer (bash)
Source files component.xml MeapNormalization.r
Usage Example with default values

Inputs

Name Type Mandatory Description
affy AffyDirectory Mandatory Affymetrix source file directory.
sampleNames CSV Mandatory Sample definitions. The table contains columns "SampleID" (key), "Filename" (relative to the Affy source directory), "Description". If some samples are not found in the source file directory, they are ignored.

Outputs

Name Type Description
normalized CSV A CSV file contains a list of path of the normalized data.

Parameters

Name Type Default Description
NProcess int 5 The number of processes are invoked in parallel execution.
annotation string "/opt/sandbox/pchen/MEAPAnnotation_Human_v62" The path of exon array annotation file.
arrayType string "exon" The type of GeneChip array ("exon": GeneChip Exon ST 1.0 array, "gene": GeneChip Gene ST 1.0 array).
metaData string (no default) The directory for storing meta data. If empty string is given, the data will be stored in the temporary folder in the execution folder, as given by Anduril and will be deleted after the execution. It is highly recommend to set this path by user. If you have large dataset, make sure there is enough space under the metaData folder.

Test cases

Test case Parameters IN
affy
IN
sampleNames
OUT
normalized
case1 properties affy sampleNames normalized

metaData=/tmp


Generated 2018-12-18 07:42:22 by Anduril 2.0.0