Simulations for BufferedMatrixMethods

Written by Ben Bolstad
email bmb@bmbolstad.com

Background

These simulations are all experimental and may not fully generalize to real-world usage. The aim is to investigate the performance of BufferedMatrixMethods and find potential areas for improvement. Work will generally be with developmental verisons of BufferedMatrixMethods. Discussion of results are usually brief notes only.

BufferedMatrix 1.3.2

These tests were all based around a collection of 2512 HGU-133 Plus 2.0 microarray CEL files. The CEL files were downloaded from the Gene Expression Omnibus. In particular the data series GSE5350 (MAQC), GSE2109, GSE2125, GSE2634, GSE2677, GSE2817 and GSE3526.

The test machine was configured with an AMD 5600+ processor, 8GB of RAM, 10GB of swap memory and Fedora 8.

R and its package configuration was as follows:
R version 2.7.0 Under development (unstable) (2008-02-02 r44303)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] affy_1.17.3 preprocessCore_1.1.5
[3] affyio_1.7.13 Biobase_1.17.9
[5] BufferedMatrixMethods_1.3.2 BufferedMatrix_1.3.0

Simulation 1

Simulation 2

Simulation 3

Simulation 3

BufferedMatrix 1.3.5

These tests were all based around a collection of 2512 HGU-133 Plus 2.0 microarray CEL files. The CEL files were downloaded from the Gene Expression Omnibus. In particular the data series GSE5350 (MAQC), GSE2109, GSE2125, GSE2634, GSE2677, GSE2817 and GSE3526.

The test machine was configured with an AMD 5600+ processor, 8GB of RAM, 10GB of swap memory and Fedora 8.

R and its package configuration was as follows:
R version 2.7.0 Under development (unstable) (2008-02-02 r44303)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] affy_1.17.3 preprocessCore_1.1.5
[3] affyio_1.7.13 Biobase_1.17.9
[5] BufferedMatrixMethods_1.3.5 BufferedMatrix_1.3.0

RMAExpress Console Application 1.0 beta 8 was built from source and used for comparison purposes in these simulations.

Simulation 1

Simulation 2