Statistics and Computational Biology

Data Sets:

This page gives pointers to data sets that we have (re)analyzed in our papers. We provide the data exactly in the form in which we have used them ourselves (i.e. including our preprocessing, calibration etc.) in order to facilitate reproducibility. For further information concerning the raw data please consult the original authors and sources.

From Zuber and Strimmer, 2010 (car score) and 2009 (cat score):

• See the care R package. Lu et al. (2004) brain aging gene expression data: lu2004.
• Sreekumar et al. (2009) Prostate cancer metabolomic data: sreekumar2009.rda.gz.

From Opgen-Rhein and Strimmer, 2007a (VAR network) and 2007b (approximate causal network):

• See the GeneNet R package. Smith et al. (2004) A. thaliana time series data: arth-smith2004.rda.gz (all genes) and 800 selected periodic genes.
• See also the R script for computing an approximate causal network and the R code for estimating the VAR network.

From Opgen-Rhein and Strimmer, 2007 (shrinkage t statistic):

• Cope et al. (2004) Affymetrix spike-in data: affyspike.rda.gz.
• See the st R package. Choe et al. (2005) "golden spike" experiment: choedata.
• van 't Wout et al. (2003) HIV-1 data: vantwout-hiv1.rda.gz.

From Boulesteix and Strimmer, 2005 (PLS transcription factor prediction):

• Kao et al. (2004) Ecoli experiment: kaoecoli.rda.gz.
• Liao et al. (2003) hemoglobin data: hemoglobin.rda.gz.
• Spellmann et al. (1998) and Gasch et al. (2000) yeast data, with compatible Lee et al. (2002) ChIP matrix: yeast-tfa.rda.gz.
• Use this R script to check that you retrieved the complete set of data.

From Wichert, Fokianos and Strimmer, 2004 (identification of cell cycle genes):

• Cho et al. (2001) human fibrolast data: fibroblasts.rda.gz.
• See the GeneCycle R package. Laub et al. (2000) caulobacter data: caulobacter.
• Spellmann et al. (1998) yeast data: spellmann-yeast.rda.gz.
• Whitfield et al. (2002) human HeLa data: humanhela.rda.gz.
• Use this R script to check that you retrieved the complete set of data.
• Table 2 of Wichert et al. (2004) can be reproduced by using this R script.

From Strimmer, 2003 (quasi-likelihood approach):

• Golub et al. (1999) leukemia data: golub.rda.gz.

From other diverse papers:

• See the longitudinal R package. Rangel et al. (2004) human T-cell data: tcell.
• Hedenfalk et al. (2001) breast cancer data: hedenfalk.rda.gz.
• Hedges (1994) alignment: amniotes-seqs.txt and amniotes-info.txt.
• See the GeneNet R package. Schmidt-Heck et al. (2004) E. coli data: ecoli.
• Tanaka et al. (2004) HCV tree: hcv.tre (Newick tree).
• West et al. (2001) breast cancer data: westdataclean.rda.gz.
• See the ape R package. Yusim et al. (2001) HIV-1 tree: hivtree.

If you miss a data set that we have analyzed in our papers please send email, and we will add it here.

Using The Data:

Note that most of the data have been prepared for analysis using R:

• The suffix "rda.gz" denotes a compressed R data file. This can be read in using the "load()" command. It is not necessary to uncompress the file beforehand.
• The "data()" command has to be used to read in data that that are part of an R package.