CARMAweb 1.6
What's new in CARMAweb 1.5
  • CARMAweb release 1.6: March 2016.
  • CARMAweb 1.6 uses R version 3.2.3 with Bioconductor 3.2.
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    Citing CARMAweb
    Rainer J., Sanchez-Cabo F., Stocker G., Sturn A. and Trajanoski Z. CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis
    Nucleic Acids Research, 2006 vol 34(Web Server Issue):W498-503.
    CARMAweb microarray analysis workflow
    The analysis of microarray data can be split up into the 3 main parts Preprocessing,Detection of differentially expressed genes and high level analysis. Not all of these analysis steps have to be performed in a microarray analysis, nevertheless it is important to provide them in one tool.
    The picture above shows how this analysis workflow is modeled in CARMAweb and how the different components can be linked together. The central part is the Data directory. All files listed there can be used as input for a new analysis step. After each analysis step the results can be returned to this Data directory, or further analyses can be performed directly on the result files from a previous step.
    Comprehensive R based Microarray Analysis web frontend
    User guide for CARMAweb: User Guide
    CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays.
    The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages.
    The web application bases on the Java 2 Enterprise Edition (J2EE) including Java Servlets and JSP technology, the Jakarta Struts framework and Enterprise Java Beans (EJB). As a interface between Java and R the Rserve package is used.
    BioConductor packages used:
  • affy: Affymetrix normalization
  • gcrma: Affymetrix normalization
  • annaffy: annotation of Affymetrix probe sets
  • limma: two color microarray normalization
  • vsn: Variance stabilizing normalization
  • multtest: statistical tests to detect differentially expressed genes and correction methods for multiple testing
  • siggenes: Significance Analysis of Microarrays (SAM)
  • maDB: utility and plotting functions
  • GOstats: statistical tests on GO ontologies

    • Special thanks to all BioConductor developers!
    CARMAweb News
    CARMAweb version: 1.6.0
    30.03.2016 Up and alive again! Moved CARMAweb to a new server, updated the R calculation backend.
  • Add support for HuGene 2.1, MoGene 2.1 and RaGene 2.1 GeneChips.
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    28.07.2014 Added support for Affymetrix Human Gene 2.0 ST GeneChips.
    22.11.2013 Solved a bug that prevented probeset ids to be returned for PrimeView microarrays.
    18.10.2013 Added support for Affymetrix Mouse Gene 2.0 ST GeneChips.
    19.09.2013 Added support for Affymetrix Rat Gene 2.0 ST GeneChips.
    07.03.2013 Fixed a bug resulting in an error when preprocessing using justRMA or justGCRMA.
    05.04.2012 Added support for Affymetrix custom SNOWBALLs GeneChips.
    09.03.2012 Added support for Affymetrix PrimeView GeneChips.
    29.02.2012 Disabled zipping of the results filder due to permanent problems with this feature.
    21.12.2011 Fixed a bug in the fold change analysis resulting in results tables containing only NA values.
    24.11.2011 Fixed a bug in the calculation of mean A (average expression) in the test statistics based analysis. Thanks to Benedicte Sohm for reporting the bug.
    18.08.2011 Smaller bugfixes in two color microarray analysis.
    10.03.2011 Fixed a problem with quantiles normalisation of custom input files with negative values.
    06.03.2011 Added option to loess normalise data from custom input files.
    10.02.2011 Added the possibility to exclude Agilent control feature from the analysis.
    27.01.2011 Minor updates.
    11.01.2011 Resolved a problem in the analysis of data from custom input files preventing that M and A values are added to the final results table.
    20.10.2010 Added support for Affymetrix Array Plate arrays using custom CDF packages from brainarray.
    30.05.2010 Solved a bug in the quantiles normalisation of custom input data.
    17.05.2010 Solved a bug preventing vsn normalisation of Affymetrix GeneChips with less than 300000 probes.
    30.04.2010 CARMAweb 1.5 released. Bases on R 2.11.0 and Bioconductor 2.6.
    18.07.2009 Security updates.
    17.01.2008 CARMAweb 1.4. Bases on R 2.6.0 and Bioconductor 2.1.
    04.12.2007 Minor updates.
    14.10.2007 CARMAweb 1.3 (based on R 2.5.1 and Bioconductor 2.0) online.
    07.06.2007 Start porting CARMAweb to R 2.5 and Bioconductor 2.0
    CARMAweb user accounts
    CARMAweb can be used with or without an user account. To get anonymous access click on the link below. The usage of CARMAweb without account requires users to stay online for the whole analysis time. Logging out or closing the connection deletes all files and analysis on the server.
    Personal password protected usage of CARMAweb is recommended.
    Anonymous use of CARMAweb
    To get a CARMAweb account (provides password protection of all user data and workspaces) use the Create account link on the left side of the page.