SIEVE User Guide

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2 Setting up a Procedure Framing the Data Framing the Data Use the following procedure to see the samples in Spotfire, select relevant frames from the Spotfire Gel view, and display them using the SIEVE Framing method. For more information about the framing method, see Appendix B, “Understanding the Framing Process.” To frame the data 1. Close the Spotfire window. The Set Parameters dialog box reappears and you can adjust parameters prior to framing. For information about parameter values, see “Setting Parameters” on page 12. 2. Click Next to frame the data. If you selected Show advanced progress info in the Submit Analysis view, a DOS window displays the progress of the procedure. IMPORTANT Stay in the SIEVE window when the system is processing. If you click another window or change programs, you might disrupt the processing. Spotfire opens, displaying the primary plot. Primary plot: Generated by SIEVE within Spotfire, this plot represents frames colored by the pValue to indicate significant differential expression within the frame. Consolidated plot: Made up of several hundred to several thousand frames, this plot shows frames of various colors, where darker frames (gels) indicate a more statistically significant difference. 18 SIEVE User Guide Thermo Scientific
2 Setting up a Procedure Framing the Data 3. To filter down to frames of interest, move the pValue slider in the Query Devices section on the right side of the window. If you are looking for a specific ratio, filter by pValue, retention time range, m/z range, or even intensity ratios. Low pValues indicate significant changes. Figure 10. Spotfire view with filtered pValues For more information about using the Spotfire view, see Appendix C, “Using Spotfire to View Analysis Results.” For further information about seeing and manipulating your data with Spotfire, see Spotfire Help. Thermo Scientific SIEVE User Guide 19
Page 1 and 2: XCALI-97186 Revision B July 2007 Fo
Page 3 and 4: Contents Thermo Scientific SIEVE Us
Page 5 and 6: Preface SIEVE User Guide Viewing th
Page 7 and 8: Getting a License Getting a New Lic
Page 9 and 10: Installing a New License Code Once
Page 11 and 12: Overview to SIEVE SIEVE software pe
Page 13 and 14: About the SIEVE Procedure 1 Overvie
Page 15 and 16: Setting up a Procedure The followin
Page 17 and 18: 2. Click Get Started to display exp
Page 19 and 20: 2 Setting up a Procedure Starting a
Page 21 and 22: 10. Click Add to add the files to t
Page 23 and 24: Table 1. Set Parameters dialog box
Page 25 and 26: Tips for Improving the Process Anal
Page 27: Spotfire displays a screen similar
Page 31 and 32: 2. Make changes to the parameters a
Page 33 and 34: Viewing a Saved Experiment 2 Settin
Page 35: 2 Setting up a Procedure Viewing a
Page 38 and 39: A Understanding the ChromAlign Proc
Page 46 and 47: B Understanding the Framing Process
Page 49 and 50: Using Spotfire to View Analysis Res
Page 51 and 52: Spotfire Range Sliders Frame Detail
Page 53 and 54: Protein ID View C Using Spotfire to
Page 55: Table 4. Parameter definitions for
Page 58: Index: P P parameters framing 37 se

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