My Microarray Software Comparison - Data Mining Software (Extension of Existing Data Mining Software)


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Definition of data mining software - extension of existing data mining software
Suggested readings
Data mining software - extension of existing data mining software (in alphabetical order)

[ ArrayMiner | Freeview & FreeOView | slcview | TreeView ]


 

Definition of data mining software - extension of existing data mining software

This kind software is usually existed as a plugin of comprehensive package to extend its functionality, but it can also be available as a standalone tool.

Suggested readings

    Experimental Design
  1. Glonek GF, Solomon PJ. Factorial and time course designs for cDNA microarray experiments. Biostatistics. 2004 Jan;5(1):89-111. [PubMed]
  2. Simon RM, Dobbin K. Experimental design of DNA microarray experiments. Biotechniques. 2003 Mar;Suppl:16-21 [PubMed]
  3. Kerr MK. Experimental design to make the most of microarray studies. Methods Mol Biol. 2003;224:137-47. [PubMed]
  4. Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet. 2002 Aug;3(8):579-588. [PubMed][full text][pdf][web supplement]
  5. Lee ML, Whitmore GA. Power and sample size for DNA microarray studies. Stat Med. 2002 Dec 15;21(23):3543-70. [PubMed]
  6. Hwang D, Schmitt WA, Stephanopoulos G, Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 2002 Sep;18(9):1184-93. [PubMed]
  7. Simon R, Radmacher MD, Dobbin K. Design of studies using DNA microarrays. Genet Epidemiol. 2002 Jun;23(1):21-36. [PubMed]
  8. Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics. 2001 Jun;2(2):183-201. [PubMed]
    Data mining
  1. Leung YF, Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet. 2003 Nov;19(11):649-59. [PubMed]
  2. Smyth GK, Yang YH, Speed T. Statistical issues in cDNA microarray data analysis. Methods Mol Biol. 2003;224:111-36. [PubMed]
  3. Nadon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet. 2002 May;18(5):265-71. [PubMed]
  4. Sherlock G. Analysis of large-scale gene expression data. Brief Bioinform. 2001 Dec;2(4):350-62. [PubMed]
  5. Wu TD. Analysing gene expression data from DNA microarrays to identify candidate genes. J Pathol. 2001 Sep;195(1):53-65. [PubMed]
  6. Quackenbush J. Computational genetics computational analysis of microarray data. Nat Rev Genet. 2001 Jun;2(6):418-27. [PubMed][pdf]
  7. Brazma A, Vilo J. Gene expression data analysis. FEBS Lett. 2000 Aug 25;480(1):17-24. [PubMed]

Data mining software - extension of existing data mining software (in alphabetical order)

 
Product Company/ Institute Interface/ Operating System Features Price Remarks
ArrayMiner 2 Optimal Design Windows/ Mac/ add-on to GeneSpring Proprietary genetic algorihm for clustering; a number of visualization tools; a new class of clustering algorithm is available in verion 2 check here demo download; manual;paper compare with K-means; version 2 white paper; also available as optional add-on to GeneSpring 
Freeview & FreeOView University of Ljubljana, Slovenia JAVA A java implementation with some functional enhancement of the famous Treeview program; accepting input from Cluster;  Free download;help; source code;
slcview 1.1.1 Swaine Chen,
Department of Developmental Biology, 
Stanford University		 UNIX/ Linux/ web/ Windows? (not tested)/ Mac (not tested) A perl program that will automatically take in the Cluster or XCluster and create clustergram, gene tree, and array tree images Free (GNU GPL) download;web server;
TreeView Michael Eisen's lab;Lawrence Berkeley  National Lab (LBNL) Windows 95/98/NT Cluster output visualization Free for academic user download;manual; source code; demo data; reference [PubMed][pdf][web supplement]; also available from stanford university and microarray.org


last updated: 23 Nov 2003
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