SIEVE User Guide

More documents

Recommendations

Info

A Understanding the ChromAlign Process Aligning Over Chromalign Time Shifts Aligning Over Chromalign Time Shifts See Figure 22 to understand the complexity of the alignment process by plotting the chromatographic time warping function. Although this plot uses data from a different set of control and sample files, it demonstrates the complexity of the alignment effort caused by chromatographic shifts. The average alignment score for the alignment in this figure is 0.53. Figure 22. Chromatographic time warping required to create alignment Time Warp 0 5 10 15 100 200 300 400 500 Time (Min) 34 SIEVE User Guide Thermo Fisher
Understanding the Framing Process To understand the framing process in SIEVE, consider that biomarker or differential expression experiments require comparing at least two sets of raw data files, each representing two distinct biological states (A compared to B); however, to be statistically meaningful, a well-designed biomarkers study should aim to compare multiple bioreplicates from control and treatment (disease) sets, each analyzed, ideally, multiple times as technical replicates. Furthermore, presenting the results of the typically large volume of generated data in one consolidated view improves the differential analysis. This discussion of the framing process covers the following topics: • Aligning Peaks • Finding the Highest Peaks Thermo Scientific SIEVE User Guide 35 B
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 and 28: Spotfire displays a screen similar
Page 29 and 30: 2 Setting up a Procedure Framing th
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

SIEVE User Guide

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?