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Bioconductor Changlog.
Tue, 13 Oct 2009
ArrayExpress
Does not replace 0 by NA anymore
?\195?\130add the phenoData
[/ArrayExpress] permanent link
ArrayExpress
Divided the main function ArrayExpress into two functions:
- getAE to download and unzip the archive from the database.
- magetab2bioc to convert mage tab files into bioconductor object even
if the files are stored locally.
- The function AEproc2bioc, by Juok Cho, is made to deal with processed data.
[/ArrayExpress] permanent link
ArrayExpress
Fix the special character from the man page
[/ArrayExpress] permanent link
ArrayExpress
Add man pages for processed data functions
Fix man pages and namespace
[/ArrayExpress] permanent link
ArrayExpress
expression values of processed ExpressionSet are numeric
[/ArrayExpress] permanent link
ArrayExpress
Uncomment the example in man.
[/ArrayExpress] permanent link
ArrayExpress
queryAE input more complete, http instead of ftp, HTTPUserAgent with name of the package for tracking pruposes
[/ArrayExpress] permanent link
ArrayExpress
fix a small problem in extract.zip
Should work even on file names not starting by E-, need to test after Mohammad changes
Use of unzip instead of int.unzip
[/ArrayExpress] permanent link
ArrayExpress
Change save settings, FALSE by default
[/ArrayExpress] permanent link
ArrayExpress
Clearer error messages
[/ArrayExpress] permanent link
ArrayExpress
Handling of multiple array design
[/ArrayExpress] permanent link
ArrayExpress
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/ArrayExpress] permanent link
ArrayExpress
A new package by Audrey Kauffmann to access the ArrayExpress Repository
[/ArrayExpress] permanent link
ArrayExpress
add the QT_list.txt file in inst/doc
Major changes that allow the package to cover most of the database
[/ArrayExpress] permanent link
ArrayExpress
add argument extract to getAE and extract_path to extract.zip
[/ArrayExpress] permanent link
ArrayExpress
- Corrected the attachment of the phenoData to the object when multiple
ADF files
- The XML package is now in Imports not in Depends
[/ArrayExpress] permanent link
ArrayExpress
Fix the problem with the path in getAE and extract.zip
[/ArrayExpress] permanent link
ArrayExpress
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/ArrayExpress] permanent link
ArrayExpress
Made shorter examples to improve time of the check
[/ArrayExpress] permanent link
ArrayExpress
Corrections to man pages
[/ArrayExpress] permanent link
ArrayExpress
Add functions getcolproc and procset to handle processed data. Only works on simple cases so far.
[/ArrayExpress] permanent link
ArrayExpress
Always numerics values, and function getcolraw to extract possible column names and avoid downloading twice when setting rawcol is needed.
[/ArrayExpress] permanent link
ArrayExpress
Minor changes to code mostly on cleaning up after usage. Used some patches from Andrew Tikhonov.
[/ArrayExpress] permanent link
ArrayExpress
More comprehensive man pages and vignettes. Add the queryAE function to answer the reviewer comments.
[/ArrayExpress] permanent link
ArrayExpress
Delete the files copied from the website when an error occurs and kills
the program.
[/ArrayExpress] permanent link
ArrayExpress
Correct extract.zip.r to make it work on Windows
[/ArrayExpress] permanent link
ArrayExpress
Set the arguments of download.file and extract.zip so that it works under Windows
[/ArrayExpress] permanent link
ArrayExpress
Full analysis as an example in the vignette
[/ArrayExpress] permanent link
ArrayExpress
Made files for processed functions
Change arguments of functions
[/ArrayExpress] permanent link
ArrayExpress
CEL and cel files are treated as AffyBatch
[/ArrayExpress] permanent link
ArrayExpress
Add the phenoData to Affy objects created with ArrayExpress and add the save argument to the ArrayExpress2 function
[/ArrayExpress] permanent link
ArrayExpress
Check that array data exists in the phenodata in the build.es function
[/ArrayExpress] permanent link
ArrayExpress
Fix problem with Feature Extraction and error messages clearer for dyes in separate files
[/ArrayExpress] permanent link
ArrayExpress
Add functions, help files, namespace and vignette
[/ArrayExpress] permanent link
ArrayExpress
Replace sampleNames(dat) by sampleNames(dat) for NChannelSet
[/ArrayExpress] permanent link
ArrayExpress
Standardizing reference to Artistic License 2.0.
[/ArrayExpress] permanent link
ArrayExpress
Remove the ArrayExpress2 function which becomes useless
Extend ArrayExpress function to other data types than affy. Functions based on the QT and the scanner name.
[/ArrayExpress] permanent link
ArrayExpress
?\195?\130?\194?\163Change default tempoutdir
[/ArrayExpress] permanent link
ArrayExpress
Add field PubMed ID and release date to experimentData
[/ArrayExpress] permanent link
ArrayExpress
Better output from queryAE
[/ArrayExpress] permanent link