sam.plot {siggenes} | R Documentation |
This functions performs a SAM or a SAM-Wilc analysis, respectively, for a specific threshold Delta, and (optionally) stores information on the differentially expressed genes in a file.
sam.plot(sam.out,delta,data,q.values=TRUE,R.fold=TRUE,na.rm=FALSE,pty.square=TRUE,file.out=NA, col.accession=NA,col.gene.name=NA,use.numbers=sam.out$use.numbers,rand=sam.out$rand)
sam.out |
the object to which the output of a previous analysis with
sam or sam.wilc was stored. |
delta |
the value of the threshold Delta for which the analysis should be performed. |
data |
the used data set. If the fold change should be computed, this data set
can be a transformed version of the data set used in the previous analysis
with sam or sam.wilc . |
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. |
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. |
pty.square |
if TRUE (default), a square SAM Plot will be generated with
x and y axes having the same range. |
file.out |
if specified (i.e. not NA ), general information like the number
of significant genes and the estimated FDR and gene-specific information is
stored in the corresponding file. |
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. |
use.numbers |
if TRUE , the number of observations that correspond to a point
in the SAM Plot will be used as symbol for this point. Will only be used, if
sam.out contains the results of sam.wilc . |
rand |
if specified, the random number generator is set in a reproducible state.
By default, the same set.seed is used as in the previous analysis with
either sam or sam.wilc |
a SAM Plot for the specified Delta and (optionally) an output file containing general information like the number of significant genes and the FDR and information about the differentially expressed genes like their names, q-values and fold changes.
vec.fdr |
a list containing the number of p0, significant genes, the FDR etc. for the specified Delta. |
sam.output |
a table containing gene-specific information about the differentially expressed genes like their IDs (i.e. the rows of the data set that contain the expression data of these genes), their expression score, q-values, the fold changes etc. |
row.sig.genes |
vector that consists of the rows of the data set that contain the expression data of the differentially expressed genes. |
Holger Schwender holger.schw@gmx.de
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response, PNAS, 98, 5116-5121.
Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genome-wide experiments, Technical Report, Department of Statistics, Stanford University.
Schwender, H. (2003). Assessing the false discovery rate in a statistical analysis of gene expression data, Chapters 5 and 6, Diploma thesis, Department of Statistics, University of Dortmund, http://de.geocities.com/holgerschw/thesis.pdf.