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 column 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.