InstallBrainArrayPackage


    Path to an example CEL file. The Affymetrix version name will be extracted from this file.


celFilePath


    Version of BrainArray (for example, "17.1.0") you want to download. 


version


    Abbreviated name (for example, "hs" = homo sapiens, "mm" = mus musculus, "gg" = gallus gallus) of the organism for which the microarrays are designed.


organism


    Abbreviated name of the annotation source (for example, "entrezg" = Entrez Gene, "ensg" = Ensembl Gene) you want to use. 


annotationSource


  When processing Affymetrix microarrays, users can specify alternative probe/gene mappings via the probeSummaryPackage parameter. Users can download such packages directly from the BrainArray web site and install them manually. Or they can use this helper function to download and install them in a single step.


SCAN is a microarray normalization method to facilitate
personalized-medicine workflows. Rather than processing
microarray samples as groups, which can introduce biases and
present logistical challenges, SCAN normalizes each sample
individually by modeling and removing probe- and array-specific
background noise using only data from within each array. SCAN
can be applied to one-channel (e.g., Affymetrix) or two-channel
(e.g., Agilent) microarrays. The Universal exPression Codes
(UPC) method is an extension of SCAN that estimates whether a
given gene/transcript is active above background levels in a
given sample. The UPC method can be applied to one-channel or
two-channel microarrays as well as to RNA-Seq read counts.
Because UPC values are represented on the same scale and have
an identical interpretation for each platform, they can be used
for cross-platform data integration.

Stephen R Piccolo

SCAN.UPC

Single-channel array normalization (SCAN) and Universal
exPression Codes (UPC)

InstallBrainArrayPackage function

Path to an example CEL file. The Affymetrix version name will be extracted from this file.

Version of BrainArray (for example, "17.1.0") you want to download.

Abbreviated name (for example, "hs" = homo sapiens, "mm" = mus musculus, "gg" = gallus gallus) of the organism for which the microarrays are designed.

Abbreviated name of the annotation source (for example, "entrezg" = Entrez Gene, "ensg" = Ensembl Gene) you want to use.

When processing Affymetrix microarrays, users can specify alternative probe/gene mappings via the probeSummaryPackage parameter. Users can download such packages directly from the BrainArray web site and install them manually. Or they can use this helper function to download and install them in a single step.

InstallBrainArrayPackage: Helper function for installing BrainArray packages

Description

Usage

Arguments

Value

Examples