| Title: | Affyhgu133Plus2Expr (GPL570) Expression Data Package |
|---|---|
| Description: | Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. |
| Authors: | Zhicheng Ji, Hongkai Ji |
| Maintainer: | Zhicheng Ji <[email protected]> |
| License: | GPL (>=2) |
| Version: | 1.47.1 |
| Built: | 2026-10-10 10:34:29 UTC |
| Source: | https://git.bioconductor.org/packages/Affyhgu133Plus2Expr |
Contains gene expression profiles from Affymetrix Human Genome U133 Plus 2.0 Array (GPL570). This package is primarily designed for GSCA (Gene Set Context Analysis). All gene expression data are downloaded from NCBI GEO. Gene expression data were preprocessed and normalized consistently using fRMA. Gene expression values are further standardized using gene expression barcode approach. The biological context of each sample was recorded and manually verified based on the sample description in GEO. Gene expression profiles are stored as hdf5 format.
| Package: | Affyhgu133Plus2Expr |
| Type: | Package |
| Version: | 1.0.0 |
| Date: | 2014-4-9 |
| License: | GPL 2.0 |
Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji <[email protected]>
McCall M.N., Bolstad B.M., and Irizarry R.A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11, 242-253.
McCall, M. N., Uppal, K., Jaffee, H. A., Zilliox, M. J., & Irizarry, R. A. (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic acids research, 39(suppl 1), D1011-D1015.
Barrett T., et al. (2007) NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucl. Acids Res. 35, D760-D765.
The data set contains 5153 human profiles on 19944 genes downloaded from NCBI GEO. Gene expression data were preprocessed and normalized consistently using fRMA. Gene expression values are further standardized using gene expression barcode approach. The biological context of each sample was recorded and manually verified based on the sample description in GEO. The gene expression value matrix is stored in hdf5 format using rhdf5 package.
This data package contains expression values of 19944 genes and 5153 samples measurements from NCBI GEO obtained using the GPL570 platform. Gene expression data were preprocessed and normalized consistently using fRMA. Gene expression values were further standardized using gene expression barcode approach. Probesets that corresponds to the same gene are averaged, so that each gene uniquely matches to one row in the database. The biological context of each sample was also recorded and manually verified based on the sample description in GEO. To enhance the reading speed of the dataset, the gene expression value matrix is stored in a hdf5 format using rhdf5 package. The rows of the matrix represents samples and the columns of the matrix represent genes. Notice that all values are 1000 times the actual value so that the values can be stored as integers to minimize file size and reading time. The package is specifically designed to be manipulated by GSCA package so users are not expected to read the expression values by themselves. The sample id, sample type, and experiment id for each sample in the gene expression compendium are also included in this data package.
www.ncbi.nlm.nih.gov/geo/
McCall M.N., Bolstad B.M., and Irizarry R.A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11, 242-253.
McCall, M. N., Uppal, K., Jaffee, H. A., Zilliox, M. J., & Irizarry, R. A. (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic acids research, 39(suppl 1), D1011-D1015.
Barrett T., et al. (2007) NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nuscl. Acids Res. 35, D760-D765.
Contains the sample id, sample type, and experiment id for each sample in the Affymetrix Human hgu133a Array (GPL570) gene expression compendium.
data(Affyhgu133Plus2Exprtab)data(Affyhgu133Plus2Exprtab)
A data frame with 5153 observations on the following 3 variables.
SampleIDa character vector
ExperimentIDa character vector
SampleTypea character vector
SampleID is a GSM ID that NCBI GEO uses to as a sample identifier. ExperimentID is a GEO ID that NCBI GEO uses to identify an experiment. SampleType denotes the cell type or tissue and whether the sample is given a specific treatment or in a specific condition.
www.ncbi.nlm.nih.gov/geo/
McCall M.N., Bolstad B.M., and Irizarry R.A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11, 242-253.
McCall, M. N., Uppal, K., Jaffee, H. A., Zilliox, M. J., & Irizarry, R. A. (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic acids research, 39(suppl 1), D1011-D1015.
Barrett T., et al. (2007) NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucl. Acids Res. 35, D760-D765.
## Load the reference table data(Affyhgu133Plus2Exprtab) str(Affyhgu133Plus2Exprtab)## Load the reference table data(Affyhgu133Plus2Exprtab) str(Affyhgu133Plus2Exprtab)