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