| Type: | Package |
| Title: | Gene Expression Datasets for the 'MM2S' Package |
| Version: | 1.0.3 |
| Date: | 2019-03-15 |
| Author: | Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca> |
| Maintainer: | Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca> |
| Description: | Gene Expression datasets for the 'MM2S' package. Contains normalized expression data for Human Medulloblastoma ('GSE37418') as well as Mouse Medulloblastoma models ('GSE36594'). Deena Gendoo et al. (2015) <doi:10.1016/j.ygeno.2015.05.002>. |
| License: | GPL-3 |
| Depends: | R (≥ 2.10), Biobase |
| Suggests: | knitr |
| VignetteBuilder: | knitr |
| biocViews: | MM2S, ExperimentData,ExpressionData, MicroarrayData |
| RoxygenNote: | 6.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2019-03-15 15:43:53 UTC; gangesh |
| Repository: | CRAN |
| Date/Publication: | 2019-03-16 00:14:26 UTC |
Normalized gene expression data for Mouse MB samples (from GSE36594).
Description
Gene expression for 20 GTML Medulloblastoma mouse samples, normalized using expresso and BrainArray CDFs (see references for details).
PLEASE NOTE: The full processed GSE36594 dataset, which contains 56 samples, can be accessed from the following locations: https://github.com/DGendoo/MM2Sdata http://www.pmgenomics.ca/bhklab/software/mm2s
Usage
data(GSE36594Expr)Value
Data and annotations are organized in a ExpressionSet of the package Biobase.
pData |
phenoData containing mouse sample genotype and origin |
exprs |
ExpressionSet with 23783 EntrezIds and 20 samples |
fData |
List of 23783 EntrezIds |
Source
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36594
References
Gendoo, D. M., Smirnov, P., Lupien, M. & Haibe-Kains, B. Personalized diagnosis of medulloblastoma subtypes across patients and model systems. Genomics, doi:10.1016/j.ygeno.2015.05.002 (2015)
Manuscript URL: http://www.sciencedirect.com/science/article/pii/S0888754315000774
Examples
data(GSE36594Expr)
# To install from github, please run the following commands in your R terminal:
# library(Biobase)
# library(devtools)
# install_github(repo="DGendoo/MM2Sdata")
# data(GSE36594Expr)
Normalized gene expression data for Human MB (GSE37418).
Description
Gene expression for 10 primary Medulloblastoma human samples, normalized using expresso and BrainArray CDFs (see references for details).
PLEASE NOTE: The full processed GSE37418 dataset, which contains 76 samples, can be accessed from the following locations: https://github.com/DGendoo/MM2Sdata http://www.pmgenomics.ca/bhklab/software/mm2s
Usage
data(GSE37418Expr)Value
Data and annotations are organized in a ExpressionSet of the package Biobase.
pData |
phenoData containing human sample MB subgroup (obtained from GEOquery of the GSE37418) |
exprs |
ExpressionSet with 19764 EntrezIds and 10 samples |
fData |
List of 19764 EntrezIds |
Source
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37418
References
Gendoo, D. M., Smirnov, P., Lupien, M. & Haibe-Kains, B. Personalized diagnosis of medulloblastoma subtypes across patients and model systems. Genomics, doi:10.1016/j.ygeno.2015.05.002 (2015)
Manuscript URL: http://www.sciencedirect.com/science/article/pii/S0888754315000774
Examples
data(GSE37418Expr)
# To install from github, please run the following commands in your R terminal:
# library(Biobase)
# library(devtools)
# install_github(repo="DGendoo/MM2Sdata")
# data(GSE37418Expr)