mt.teststat {multtest}  R Documentation 
These functions provide a convenient way to compute test statistics, e.g., twosample Welch tstatistics, Wilcoxon statistics, Fstatistics, paired tstatistics, block Fstatistics, for each row of a data frame.
mt.teststat(X,classlabel,test="t",na=.mt.naNUM,nonpara="n") mt.teststat.num.denum(X,classlabel,test="t",na=.mt.naNUM,nonpara="n")
X 
A data frame or matrix, with m rows corresponding to variables
(hypotheses) andn columns to observations. In the case of gene
expression data, rows
correspond to genes and columns to mRNA samples. The data can
be read using read.table .

classlabel 
A vector of integers corresponding to observation (column)
class labels. For k classes, the labels must be integers
between 0 and k1. For the blockf test option,
observations may be divided into
n/k blocks of k observations each. The observations are
ordered by block, and within each block, they are labeled using the
integers 0 to k1.

test 
A character string specifying the statistic to be
used to test the null hypothesis of no association between the
variables and the class labels. If test="t" , the tests are based on twosample Welch tstatistics
(unequal variances). If test="t.equalvar" , the tests are based on twosample
tstatistics with equal variance for the two samples. The
square of the tstatistic is equal to an Fstatistic for k=2. If test="wilcoxon" , the tests are based on standardized rank sum Wilcoxon statistics.If test="f" , the tests are based on Fstatistics.If test="pairt" , the tests are based on paired tstatistics. The
square of the paired tstatistic is equal to a block Fstatistic for k=2. If test="blockf" , the tests are based on Fstatistics which
adjust for block differences
(cf. twoway analysis of variance).

na 
Code for missing values (the default is .mt.naNUM=93074815.62 ).
Entries with missing values will be ignored in the computation,
i.e., test statistics will be based on a smaller sample size. This
feature has not yet fully implemented.

nonpara 
If nonpara ="y", nonparametric test statistics are computed based on ranked data. If nonpara ="n", the original data are used. 
For mt.teststat
, a vector of test statistics for each row (gene).
For mt.teststat.num.denum
, a data frame with
teststat.num 
the numerator of the test statistics for each row, depending on the
specific test option. 
teststat.denum 
the denominator of the test statistics for each row, depending on the
specific test option. 
Yongchao Ge, yongchao.ge@mssm.edu,
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
# Gene expression data from Golub et al. (1999) data(golub) teststat<mt.teststat(golub,golub.cl) qqnorm(teststat) qqline(teststat) tmp<mt.teststat.num.denum(golub,golub.cl,test="t") num<tmp$teststat.num denum<tmp$teststat.denum plot(sqrt(denum),num) tmp<mt.teststat.num.denum(golub,golub.cl,test="f")