sam, sam.dstat,
sam.wilc and sam.snp.d:"numeric" representing the
expression scores of the genes.d.bar:"numeric" representing
the expected expression scores under the null hypothesis.vec.false:"numeric" containing
the one-sided expected number of falsely called genes.p.value:"numeric" consisting of
the p-values of the genes.s:"numeric" representing the
standard deviations of the genes. If the standard deviations are
not computed, s will be set to numeric(0). s0:"numeric" representing the
value of the fudge factor. If not computed, s0 will be
set to numeric(0).mat.samp:"matrix" containing
the permuted group labels used in the estimation of the null
distribution. Each row represents one permutation, each column
one observation (pair). If no permutation procedure has been used,
mat.samp will be set to matrix(numeric(0)).p0:"numeric" representing the
prior probability that a gene is not differentially expressed.mat.fdr:"matrix" containing general
information as the number of significant genes and the estimated FDR
for several values of $Delta$. Each row represents one
value of $Delta$, each of the 9 columns one statistic.q.value:"numeric" consisting of
the q-values of the genes. If not computed, q.value will be
set to numeric(0).fold:"numeric" representing the
fold changes of the genes. If not computed, fold will be
set to numeric(0).msg:"character" containing information
about, e.g., the type of analysis. msg is printed when the functions
print and summary, respectively, are called.chip:"character" naming the microarray
used in the analysis. If no information about the chip is available,
chip will be set to "".signature(x = "SAM"): After generating a SAM plot,
identify can be used to obtain information about the genes by
clicking on the symbols in the SAM plot. For details, see
help.sam(identify). Arguments are listed by args.sam(identify).signature(x = "SAM"): Generates a SAM plot or the Delta
plots. If the specified delta in plot(object,delta) is
a numeric value, a SAM plot will be generated. If delta is either
not specified or a numeric vector, the Delta plots will be generated.
For details, see ?sam.plot2, ?delta.plot or
help.sam(plot),respectively. Arguments are listed by args.sam(plot).signature(x = "SAM"): Prints general information such as
the number of significant genes and the estimated FDR for a set of
$Delta$. For details, see help.sam(print). Arguments are
listed by args.sam(print).signature(object = "SAM"): Shows the output of the SAM
analysis.signature(object = "SAM"): Summarizes the results of
a SAM analysis. If delta in summary(object,delta) is not
specified or a numeric vector, the information shown by print and some
additional information will be shown. If delta is a numeric
vector, the general information for the specific $Delta$ is
shown and additionally gene-specific information about the genes called
significant using this value of $Delta$. The output of summary
is an object of class sumSAM which has the slots row.sig.genes,
mat.fdr, mat.sig and list.args. For details,
see help.sam(summary). All arguments are listed by args.sam(summary).Schwender, H. (2004). Modifying Microarray Analysis Methods for Categorical Data -- SAM and PAM for SNPs. To appear in: Proceedings of the the 28th Annual Conference of the GfKl.
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
sam,args.sam,sam.plot2,
delta.plot