Statistics Committee report. Jean-Louis Laffont
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1 Statistics Committee report Jean-Louis Laffont
2 STA Committee membership: Chair: Jean-Louis Laffont France Vice: Kirk Remund USA Members: Julia Barabas Hungary Gabriel Carré France Olfat H. El Bagoury Egypt Mustapha El Yakhlifi France Mohamed Hanafi France Bonnie Hong USA Winfried Jackisch Germany Zivan Karaman France Tim Perez USA Ray Shillito USA Bo-Jein Kuo Separate Custom Territory of Taiwan, Penghu, Kinmen and Matsu
3 Outline Overview of support activities from June 2015 to June 2016: Report reviews Statistical analyses Support to GMO Committee Consulting Statistical tools Workshops/Meetings Support to Variety Committee Working programme
4 Report reviews: 4 validation report reviews ( June 2014 June 2015: 2 test plan reviews, 1 validation report review June 2013 June 2014: June 2012 June 2013: June 2011 June 2012: June 2010 June 2011: 1 review for SST 3 test plan reviews, 8 validation report reviews 3 test plan reviews, 3 validation report reviews 4 test plan reviews, 1 validation report review 8 test plan reviews, 8 validation report reviews) Statistical analyses: 4 Method Validation studies
5 Support to GMO Committee Support for the preparation of PT21 Revised computations in Posterior predictive MS Excel calculator
6 Support to GMO Committee Review of JRC Technical Temporary Report: European Network of GMO Laboratories - Working Group Seed Testing (WG-ST) New concepts: testing plan LOD, max sample size defined from genome size for PCR methods
7 Consulting:
8 Statistical tools
9 Statistical tools:
10 Statistical tools: Number of downloads: also from:
11 Number of stat tools downloads for the period 01/06/ /05/2016 Grand total: 2117 (last year: 1883) Thank you for your interest in ISTA statistical tools!
12 Workshops No activity for the period
13 Meetings
14 Global Detection Methods and Reference Materials Symposium Minneapolis, USA October 15-16, 2015 Theory and uncertainty of sampling Kirk Remund
15 SCST SuperWorkshop IOWA State University February 8-12, 2016 Seed Testing Plans and Statistical Tools for Analysis Kirk Remund
16 Participation of Jean-Louis Laffont in UFS working group Adventitious Presence Certification regular meetings Sharing/promoting ISTA approach and tools
17 Support to Variety Committee Analysis of Comparative Tests for evaluating the performance of microsatellite markers for variety identification
18 The data Objective: We would like to know if the marker s profiles agree among labs for the different varieties in the study
19 One simple way of determining the agreement between the marker profiles provided by two laboratories is to compute the overall percentage of agreement Example: one variety Coincidence matrix overall percent agreement =. Total # of alleles: = 36 alleles have the same result in both labs 36 p 41 8 a = = 78.%
20 The problem with the overall percentage of agreement is that it doesn t take into account the agreement that would be expected purely by chance Alternative measures of agreement have been developed to avoid this problem: Cohen s kappa (1960) Fleiss kappa (1971) for more than two laboratories see Krippendorff (2004) for a review of different measures of agreement Krippendorff, K. (2004). Reliability in content analysis: some common misconceptions and recommendations. Human Communication Research 30 (3),
21 Cohen s kappa ˆ κ C = p a 1 p p e e. p a : overall percent agreement. p e : chance percent agreement Example: Coincidence matrix p a = p e = = ˆ = = κ C
22 Cohen s kappa : interpretation The range of possible values of Cohen s kappa is from -1 and : perfect agreement 0 : agreement no better than expected by chance - 1 : agreement worse than expected by chance Guidelines from Landis and Koch (1977): Landis, J.R. and G.G. Koch (1977). The measurement of observer agreement for categorical data. Biometrics 33 (1):
23 Statistical analysis of Comparative Tests (CT) results from microsatellite markers for wheat variety verification Computations have been performed with the R irr package (Gamer et al., 2012) Functions for computing various coefficients of reliability of agreement
24 Statistical analysis of wheat CT Agreement between pairs of laboratories of the marker profiles for the different varieties in the study Substantial agreement Almost perfect agreement
25 Statistical analysis of wheat CT The agreement for scoring varieties among 5 laboratories was good (Fleiss kappa computed for each variety measuring the agreement among these 5 laboratories was between and 1) Two laboratories were not in agreement with the others and the reasons for this were clearly stated by the CT organizer
26 Working programme
27 Continue support to ISTA Technical Committees regarding Validation Report reviews, Test Plan reviews, analysis of validation studies Specific support to SH Committee (e.g. update of SH PT rating tool) Specific support to GMO Committee (e.g. PTs quantitative rating, work on the handbook - PDE tool, purity checking for PBA, ) Seedcalc update for MS Excel 2007 and above Update and publication of Posterior predictive MS Excel calculator Update/maintenance of various tools (e.g. Heterogeneity Testing calculator) Specific support to PT Committee (retrospective analysis)
28 Projects Training of some TCOM representatives in Statistics for the analysis of Method Validations studies Modeling beliefs with a beta distribution defined by two points: the most likely value and the 100c % chance maximum value Bayesian Statistics Use of number theory to define exact confidence intervals of the dispersion factor in germination tests
29 ISTA/AOSA/SCST Seedcalc Workshop June 14-16, 2017 Denver, CO, USA Confirmed Lecturers: Kirk Remund, Monsanto Jean-Louis Laffont, DuPont Pioneer Topics and activities to include: Statistical distributions for seed testing Sampling principles for seed testing Seed testing plans for adventitious presence testing or low level testing using qualitative and quantitative assays Seed testing plans for purity testing Statistical outlier detection Assessing reproducibility and repeatability of both quantitative and qualitative seed assays Bayesian methods for seed testing For addition information contact: Anna Doornink, Eurofins BioDiagnostics River Falls, WI
30 Acknowledgements STA Committee members ISTA Secretariat and ISTA ECOM TCOM members Local organizers of the meeting Users of the tools developed by the STA Committee
31 Thank you for your attention Tänan teid tähelepanu eest
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