1.9.2 Correct
version of gap committed; design slot added to samroc.result
with consequences for samrocN and samrocNboot
1.9.1 bug fix in rsd.test
1.6.5 Zfreq removed
1.6.3 GSEA.mean.t added,
NAMESPACE added, permutation.t withdrawn, gap
corrected, class samroc.result added
1.5.8 one.probeset.per.gene added, as
well as GSEA.t2 and GSEA.Hotelling. The
functions nn.impute
and caha have been withdrawn. Instead the
corresponding functions
in packages impute and cclust are recommended.
1.5.7 union.of.pways added, and caha withdrawn.
1.5.6 permutation.t permits na.rate = 0.
1.5.5 restricted randomisation enabled in samrocN
1.5.3 as.vector introduced in calls
to ecdf
v
1.5.2 some minor changes to documentation
v
1.5.1 Documentation and code cleaned up to pass CRAN
requirements.
v
1.4.9 pava.fdr changed to output
results in the same order as input p-values.
Changes 1.4.6. The function normalise has been
up-dated to use proper data types. The function permutation.t corresponding to a permutation
Welch’s t-test allowing for arbitrary
missing structure has been added. The Wilcoxon test
calculation version of the Kruskal-Wallis test
function firstpass now works much faster thanks to a
reformulation in terms of Kronecker products. The
Gene Set Enrichment Analaysis tool gsea appears for
the first time in this package. A new tool for calculating FDR comes with
function pava.fdr.
The methods behind the function p0.mom
are up-dated. The function JT.test provides a Jonkheere-Terpstra trend test. A version of samrocN that uses C-code, samrocNboot, appears thanks to
the contributions of Freja Vamborg.
Finally, Ftest
now calculates p-values based on bootstrapped residuals.
Changes 1.3.4. The package has changed name to SAGx. Some changes in the linear models workhorse Xprep have increased speed considerably. Other
function like samroc will benefit from this.
Also, the function stat.bay.est.lin has been
removed since more recent code is available within sma.
A bug was discovered and corrected in the gap function, thanks to a mail
contact with Seo Young Kim, Basic
Research Institute,