| ebam {siggenes} | R Documentation |
Performs an Empirical Bayes Analysis of Microarrays for a specified value of the fudge factor a0. Modified versions of the t statistics are used.
ebam(a0.out,data,a0=NA,p0=NA,delta=NA,stable=TRUE,number.int=139,local.bin=.1,
col.accession=NA,col.gene.name=NA,q.values=TRUE,R.fold=TRUE,R.dataset=data,na.rm=FALSE,
file.out=NA)
a0.out |
the object to which the output of a previous analysis with find.a0
was assigned. |
data |
the data set that should be analyzed. Each row of this data set must
correspond to a gene. It has to be the same data set that was used in
find.a0. |
a0 |
the fudge factor. If NA, the value suggested by find.a0
will be used. |
p0 |
prior probability that a gene is differentially expressed. If not specified
(i.e. NA), it will automatically be computed. |
delta |
a gene will be called differentially expressed, if its posterior
probability of being differentially expressed is large than or equal to
delta. By default, the same delta is used as in find.a0. |
stable |
if TRUE (default), p0 will be computed by the algorithm of
Storey and Tibshirani (2003). If FALSE, the (unstable) estimate will be computed
that ensures that the posterior probability of being differentially expressed
is always nonnegative. |
number.int |
the number of equally spaced intervals that is used in the logistic regression for the estimation of the ratio of the null density to the mixture density. |
local.bin |
specifies the interval used in the estimation of the local FDR for the expression score z. By default, this interval is [z-0.1,z+0.1]. |
col.accession |
the column of data containing the accession numbers of
the genes. If specified, the accession numbers of the significant genes
will be added to the output. |
col.gene.name |
the column of data that contains the names of the genes.
If specified, the names of the significant genes will be added to the output. |
q.values |
if TRUE (default), the q-value for each gene will be computed. |
R.fold |
if TRUE (default), the fold change for each differentially
expressed gene will be computed. |
R.dataset |
the data set used in the computation of the fold change. This data
set can be a transformed version of data. |
na.rm |
if FALSE (default), the fold change of genes with at least one
missing value will be set to NA. If TRUE, missing values will be
replaced by the genewise mean. |
file.out |
if specified, general information like the number of significant genes and the estimated FDR and gene-specific information like the expression scores, the q-values, the R fold etc. of the differentially expressed genes are stored in this file. |
a plot of the expression scores against their posterior probability of being differentially expressed, and (optional) a file containing general information like the estimated FDR and the number of differentially expressed genes and gene-specific information about the differentially expressed genes like their names, their expression scores, q values and their fold changes.
FDR |
vector containing the estimated p0, the number of significant genes, the number of falsely called genes and the estimated FDR. |
ebam.out |
table containing gene-specific information about the differentially expressed genes. |
row.sig.genes |
vector consisting of the row numbers that belong to the differentially expressed genes. |
... |
The number of false positives are computed by p0 times the number of falsely called genes.
Holger Schwender, holger.schw@gmx.de
Efron, B., Tibshirani, R., Storey, J.D., and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.