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Component
MeapNormalizationPrepares 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 | ||
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metaData=/tmp |
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