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Bioconductor Changlog.
Sat, 12 Jan 2008
pdInfoBuilder
Initiated adpt to new Affymetrix format on the annotation files
[/pdInfoBuilder] permanent link
genefilter
Added a note to the manpage of genefilter regarding unequal sample sizes and IQR
Biostrings
Reworked the findPalindromes() API:
- change in terminology to align with established practices: "antipalindromes"
are now called "complemented palindromes" and "the gap" between the 2 arms
is now called "the loop";
- no more 'anti' arg: use findComplementedPalindromes() to find complemented
palindromes;
- the 'max.ngaps' arg has been renamed 'max.looplength';
- there is a new 'min.looplength' arg (not yet supported);
- there is a new 'max.mismatch' arg (not yet supported);
See ?findPalindromes for more details.
annotate
Modifications to make PWAmat() work with new pkgs
Changes were to PWAmat() and enable it to get an incidence matrix for
the newer organism based annotations as well as the older chip based
packages. Changes primarily are to allow PWAmat() to know when it has
an organism based package or chip based package so it can return the
correct result.
PGSEA
Secondary vignette should now build on all platforms (except windows)
oligo
Improving support to Affy 5.0 and 6.0