README.md

In harrisgm/rta10.probeFile: Probe sequence data for microarrays of type rta10

rta10.probeFile

Contains annotated probe-level information for the RTA-1_0 microarray. Used by the GCSscore R package for differential gene expression analysis.

Description

===================

The rta10.probeFile package is an AnnotationForge-generated package containing the probe sequence information for RTA-1_0 (Rat Transcriptome Array 1.0) array. The package contains a data.frame containing the necessary probe-level information to run the GCSscore differential expression on the following Affymetrix/Thermo-Fisher cchip type:

Rat Transcriptome Array (RTA-1_0) microarray

All probe-level information in this file was pulled from the platform design (pd) annotation package (pd.rta.1.0) on Bioconductor: https://bioconductor.org/packages/release/data/annotation/html/pd.rta.1.0.html

This probe-level package was created using the AnnotationForge package. The AnnotationForge package required the getProbeDataAffy function to be modified to correctly read in the probeFile file for newer Affymetrix array types. This modified function was saved as getProbeDataMTA. The customized functions from the AnnotationForge package can be found the following github repository: https://github.com/harrisgm/GCSscore-probeFile-functions

Additionally, the compression scheme of the rda file was set to xz with a compression level of 9. This level of compression was necessary to keep the rda beneath 100Mb.

The only column that is not directly from the platform design (pd) packages is the GC.Count column was generated by running the following commands on the full probe sequences that are pulled from the platform design packages (found in the XXXpFBuilder.R functions in the GCSscore-probeFile-functions repository:

chip.pmfeature[,GC.count := str_count(sequence, "G|C")]

The full probe sequence column was then removed and replaced just the GC.count information for each probe. The full probe sequence column was removed to reduce the resulting packag sizes to under 100Mb.

Installation

rta10.probeFile is an package that is in the process being uploaded to the BioConductor repository. Until it is uploaded to Bioconductor, the recommended way to install it is to load R and ensure that all dependencies are install prior to installation.

Dependencies from Bioconductor (run commands in Rstudio/R.app):

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AnnotationDbi")

Once the dependencies are installed, build and install the rta10.probeFile package from source.

Contact

Guy Harris, M.S. [e-mail]

Michael F. Miles, M.D., Ph.D. [e-mail]

harrisgm/rta10.probeFile documentation built on Nov. 4, 2019, 1:29 p.m.