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Microarray data analysis startup by using GeneSpring

Objectives:. Introduce terminology and interface of GeneSpringImport data filesSet up experiments for data analysis 1. Normalization 2. Parameters 3. Interpretations 4. Error modelPerform quality controlExport gene lists, graphs, clusters, and venn diagram . I. Terminolog

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Microarray data analysis startup by using GeneSpring

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    1. Microarray data analysis startup by using GeneSpring Bo Gao WSU Bioinformatics Core

    2. Objectives: Introduce terminology and interface of GeneSpring Import data files Set up experiments for data analysis 1. Normalization 2. Parameters 3. Interpretations 4. Error model Perform quality control Export gene lists, graphs, clusters, and venn diagram

    3. I. Terminology of GeneSpring

    4. II. GeneSpring Interface

    5. 1.Tool Bar Accesses GeneSpring Functions

    6. 2. Navigator a. Gene List Folder A gene list contains collections of genes that result from a particular analysis. The all genes list is automatically created and displayed containing all genes in the genome

    7. b. Experiments Folder

    8. c. Gene List Inspector Double click on a gene list to see detailed information

    9. d. Gene Inspector double click on a gene in a browser window or a gene in a gene list

    10. 3. Genome Browser

    11. 1. Prepare data for GeneSpring by using a or b, and c a. Use following steps for getting data from compact disk III. Importing Data

    12. b. Use following steps for getting data from Bioinformatics Core Data Server

    14. c. Click on Start ? Programs ? Affymetrix ? Data Transfer Tool

    18. 2. Create Data Report --- Must Do This for Each File . Open GCOS (GeneChip Operating Software) . Open a file

    29. 3. Import data into GeneSpring

    32. Add data with using each of your tab delimited (.txt) file

    36. IV. Experiment Normalization

    37. V. Defining the Experiment Parameters

    38. VI. Creating the Experiment Interpretations Determine how your experiment should be displayed

    39. VII. Creating the Experiment Error Model

    40. VIII. Quality Control Elimination of poor quality samples and genes

    46. VIIII. Export Data and Images 1. Export gene list to MS Excel by using Copy annotated gene list

    47. 2. Export browser images a. Export graphs

    49. b. Export clusters

    52. c. Create venn diagram . For gene list EXP > 100 FC > 2

    53. . For gene list EXP > 50 FC > 2.5

    54. . For gene list 99 > EXP > 50 FC > 2

    55. . For all genes

    56. d. Export venn diagram

    58. References GeneSpring user manual Pam Tang “Microarray data analysis genespring workshop” http://www.silicongenetics.com/cgi/SiG.cgi/Support/demos/index.smf

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