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BASE Quick Guide

BASE Quick Guide. Duke University Medical Center DNA Microarray Facility. This Guide will show you how to…. Log in, log out Change password Download files Read news Analysis: create experiment & BioAssaySet, view data details, filter, normalize, analyze and export data

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BASE Quick Guide

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  1. BASE Quick Guide Duke University Medical Center DNA Microarray Facility

  2. This Guide will show you how to… • Log in, log out • Change password • Download files • Read news • Analysis: create experiment & BioAssaySet, view data details, filter, normalize, analyze and export data • Add sample origin and annotation type • Edit samples • This guide also contain links to official BASE manual at the end.

  3. To Log In • Open your web browser (IE/Netscape etc.) And go to • http://base-server.duhs.duke.edu/ • Enter your user name and password • Press “Log in”

  4. To Log out • Click on “Log out”

  5. To change password • Open the “Users” menu • Click on “My account” • The “change password” section is on the bottom

  6. To Download Files • To download result file (.gpr), image (.tif, .jpg) and setting (.gps) files: • Open the “Hybridizations” menu • Click on “Scans” • Select the sample you want to download • In the “View scan” window, the download link for result file and image files are in the “Images” table.

  7. To Read News The news is located on the bottom of your login window

  8. To Add Sample Origin

  9. To add sample annotation type • For the Type filed: • Integers: whole number (e.g. time point in whole min, hours, years) • Float: for any type of large or small numeric value with or without decimals. (e.g. complex time point values, protein values) • Enum: for designing groups that a sample can belong to (e.g. protein status [positive/negative/unknow]) • Text: other types of annotations where a textual description is desired.

  10. Edit Sample (1) The microarray facility will enter sample names. To include additional information for samples, e.g. add descriptions, annotations. You need to edit your samples. Just select “Samples” from the “Biomaterials” menu, and click the sample name you want to edit.

  11. Edit Sample (2) Enter the information you want to add to the sample. If you want to add annotations, select “accept and annotate”, otherwise click Accept to finish edit sample.

  12. Edit sample (3): add annotation to sample Select the annotation type you want to add to the sample. Click update Enter/select value for the annotation Click Accept to finish adding sample annotation.

  13. Links • BASE site • http://base.thep.lu.se/ • BASE online user’s guide http://opensource.microarray.omrf.org/wiki/bin/view/BASE/BASEdBUsersGuide • BASE user’s guide, download • http://base.thep.lu.se/documentation.phtml

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