Data

• Chemores data
  1. mRNA expression (RData file): 41000×123 matrix contains normalized data of 41000 Agilent gene probes from 123 Chemores samples. And here is the gene annotation file for the Agilent probes. See the paper (Lazar et al 2013, BMC Medical Genomics) for description of the samples, tissue preparation, Agilent array technology, data normalization, etc.
  2. miRNA expression (RData file): 939×123 matrix contains normalized data of miRNA from 123 Chemores samples. See the paper (Lazar et al 2013, BMC Medical Genomics) for description of the samples, tissue preparation, Agilent array technology, data normalization, etc.
  3. clinical information (RData file): This 123×9 matrix contains data on 9 variables of the 123 Chemores samples.
• The ProSpect package contains a subset of the spike-in data used in Tan et al (Bioinformatics 2006). This is the complete set:
  1. SpikeInFull.zip: preprocessed by Ciphergen for background correction and total ion normalization (what we used in the paper),
  2. spikein_xml.zip raw uncorrected data
  3. blank(corrected)_csv.zip and blank_xml.zip: corrected and raw blank scan data
• Stockholm breast cancer and microarray data. Ref. Pawitan et al Breast Cancer Research 2005, 7:R953-R964. In several Rdatasets of MAS5 values: stockholm-U133AB.RData, stockholm-U133A.RData and Stockholm-U133A-50%.RData.
• Uppsala breast cancer microarray data: Rdata file containing MAS5 U133AB expression values of for 253 patients from Uppsala. The clinical data can be obtained from GEO repository, with accession code GSE3494. Ref Miller et al, An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. PNAS 102: 13550-13555, 2005. In several Rdatasets of MAS5 values: uppsala-U133AB.RData, uppsala-U133A.RData and uppsala-U133A-50%.RData.
• Swedish subtypes: array and clinical. Ref. Calza et al Breast Cancer Research 2006.
• Microarray Rdata examples: hedenfalk.RData, and rosenwald.RData.

Related to In all likelihood: Statistical modelling and inference using likelihood. Oxford University Press, June 2001. You can download:

• R package of programs and datasets to complement the examples
• list of known errors
• Table of Contents (postscript file)
• Sample chapters: Chapter 4 (Basic models) (ps) (pdf)