Description Usage Arguments Details Value Author(s) References See Also Examples
This function computes test statistics, e.g., tstatistics, Fstatistics, SAM, fold changes, moderated t or F statistics, B statistics, for each row of a microarray data matrix.
1 
X 
A matrix, with m rows corresponding to variables
(hypotheses) and n 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  
L 
A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0 and 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.
 
extra 
Extra parameter needed for the test specified; see

The function comp.stat
interfaces to a C function and
computes various statistics for differential expression in the C
environment and therefore faster than functions in R. However,
functions in R that are implemented in the DEDS packages may have
more flexibility in terms of specifications of arguments. Below is a
table the details comp.stat
and its equivalent R functions
in the DEDS package. Note that all the R functions listed in the 2nd
column of the table below return a function with bindings for a series
of arguments which accept the microarray data matrix as its single
argument and compute accordingly statistics.
Interface to C  R functions  Statistics 
deds.stat(X, L, test="t")  tTest(L=NULL, mu=0, var.equal=FALSE)  t statistics 
deds.stat(X, L, test="fc")  FC(L=NULL, is.log=TRUE, FUN=mean)  fold change 
deds.stat(X, L, test="sam")  Sam(L=NULL, prob=0.5, B=200, stat.only=TRUE, verbose=FALSE, deltas, s.step=0.01, alpha.step=0.01, plot.it=FALSE)  SAM statistics 
deds.stat(X, L, test="f")  fTest(L=NULL)  F statistics 
deds.stat(X, L, test="modt")  tmodTest(L=NULL)  moderated t statistics 
deds.stat(X, L, test="modf")  fmodTest(L=NULL)  moderated F statistics 
deds.stat(X, L, test="B")  BTest(L=NULL, proportion=0.01)  B statistics 
A vector of test statistics for each row of the matrix.
Yuanyuan Xiao, [email protected],
Jean Yee Hwa Yang, [email protected].
For references on Bstatistics and moderated t and F statistics:
Lonnstedt, I. and Speed, T. P. (2002). Replicated microarray data. Statistica Sinica 12, 3146.
Smyth, G. K. (2003). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. http://www.statsci.org/smyth/pubs/ebayes.pdf
deds.genExtra
,
for B statistics: lm.series
and
ebayes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21  X < matrix(rnorm(1000,0,0.5), nc=10)
L < rep(0:1,c(5,5))
# genes 110 are differentially expressed
X[1:10,6:10]<X[1:10,6:10]+1
# t statistics
tstat < comp.stat(X, L, test="t")
# SAM, fudge factor set as the median of pooled genewise standard deviations
samstat < comp.stat(X, L, test="sam")
# SAM, fudge factor set as the 90% of pooled genewise standard deviations
samstat < comp.stat(X, L, test="sam", extra=c(0.9))
# moderated t
modtstat < comp.stat(X, L, test="modt")
# B, proportion of differentially expressed genes is set at default, 1%
Bstat < comp.stat(X, L, test="B")
# B, proportion of differentially expressed genes is set at 10%
Bstat < comp.stat(X, L, test="B", extra=c(0.1))

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.