Data description

Data description

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The datasets used in the course are described here. Load them in R by:

mydata <- read.table("datafile.csv",header=TRUE,sep=";")

bosson

The spreadsheet (courtesy of Professor Jean-Luc Bosson) contains aneurysm data from 209 patients coming from France or Vietnam. The variables are:

• country: either Vietnam or France
• gender: either M or F
• aneurysm: size of aneurysm in mm
• bmi: body mass index
• risk: a number of risk factors in 0, …, 5

dimer

The spreadsheet (courtesy of Professor Jean-Luc Bosson) contains log-dimer data over 530 patients, grouped into 3 age classes. The variables are:

• log.dimer: logarithm of d-dimer indices (an indicator for the risk of thrombosis)

• age: the age class in 1 (younger than 50), 2 between 50 and 70, 3 older than 70.

feretti

The spreadsheet (courtesy of Professor Gilbert Ferretti) contains data from 43 patients with lung tumor. The variables are:

• height: the height of the tumor in mm

• diameter: the largest diameter of the tumor in mm

• density: the apparent density in negative (less dense than water), null (as dense as water), positive (denser than water)

• invasive: whether the tumor was invasive (yes or no).

fires

Data on 270 forest fires in Portugal from P. Cortez and A. Morais The variables are:

• month

• day

• temp: the temperature in Celsius degrees

• relhum: the relative humidity in percentage

• wind: the wind speed in km/h

• area: the burned area in hectares.

LenzT, LenzI

Lenz et al.'s transcriptome and clinical data on 414 patients with diffuse large B cell lymphoma (GSE10846). LenzT is a transcriptome data matrix over 17290 protein coding genes. LenzI contains 10 variables of clinical information for the same patients.

LenzT is a numeric matrix of size 414 x 17290. The columns are named by gene symbols, the rows by GSM numbers.

LenzI is a matrix 414 x 10, rows are named by the same GSM numbers as LenzT. Columns are:

• gender: character in male, female

• age : numeric

• diagno: diagnosis described by ABC (activated B-cell Double-Hit Diffuse Large B-Cell Lymphoma), GCB (germinal center B-cell Double-Hit Diffuse Large B-Cell Lymphoma), Unclassified

• status: character in alive, dead

• follup: follow up time

• regim: type of chemotherapy: CHOP CHOP-Like Regimen, R-CHOP R-CHOP-Like Regimen

• ecog: ECOG performance status (0 to 4)

• stage: stage of lymphoma (1 to 4)

• ldhrat: effusion lactate dehydrogenase (LDH)/serum ratio

• extnod: number of extranodal sites (0 to 5)

The transcriptome matrix LenzT has been transformed using function rename, the gene symbols match those of dicoH.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846

References

Lenz G, Wright G, Dave SS, Xiao W et al. Stromal gene signatures in large-B-cell lymphomas. N Engl J Med 2008 Nov 27;359(22):2313-23.

Cardesa-Salzmann TM, Colomo L, Gutierrez G, Chan WC et al. High microvessel density determines a poor outcome in patients with diffuse large B-cell lymphoma treated with rituximab plus chemotherapy. Haematologica 2011 Jul;96(7):996-1001.

tauber

The spreadsheet (courtesy of Professor Ma"{}t'e Tauber) contains heights and weights of 2891 children from 4 to 7 years old. The variables are:

• gender: male (M) or female (F)

• age: in months

• height: in centimeters

• weight: in kilograms. Convert centimeters to inches, dividing by 2.54. Convert kilograms to pounds, multiplying by 2.2064.