README.md

In harrisgm/mta10probe: Probe sequence data for microarrays of type mta10

mta10probe

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

The mta10probe package is an AnnotationForge-generated package containing the probe sequence information for MTA-1_0 (ClariomD mouse) array. The package contains a data.frame containing the full Affymetrix/Thermo-Fisher "probe.tab" file.

The original probe.tab file can be found downloaded from the Affymetrix website: http://www.affymetrix.com/Auth/analysis/downloads/lf/xta/MTA-1_0/MTA-1_0.mm10.probe.tab.zip

The original probe.tab file can also be found on the Thermo-Fisher website: https://sec-assets.thermofisher.com/TFS-Assets/LSG/Support-Files/MTA-1_0-mm10-probe-tab.zip

The AnnotationForge package required the getProbeDataAffy function to be modified to correctly read in the probe_tab file for newer Affymetrix array types. This modified function was saved as getProbeDataMTA. This function can be uploaded if desired.

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, while still containing the full probe_tab file.

Installation

mta10probe 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 mta10probe package from source.

Contact

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

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

harrisgm/mta10probe documentation built on Nov. 4, 2019, 1:29 p.m.