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AmericanIdiomsSlang16Apr2007
a day late and a dollar short adjective Definition: (idiomatic) action that was taken too late and too feeble to be of any use, not enough to be useful ...
AmericanIdiomsSlang16Mar2007
get the hell out of dodge Meaning: (idiomatic) to leave or get out (of anywhere) at once Origin: The phrase is a reference to Dodge City, Kansas. Dodge City ...
AmericanIdiomsSlang1Aug2007
a different ballpark noun Definition: (idiomatic) something totally unrelated or of a vastly different scale or scope. Example: Playing Flight Sim ...
AmericanIdiomsSlang1Mar2007
1. a cut above adjective Definition: (idiomatic) superior to; of a higher quality than Examples: She really thinks she's a cut above in that hat. ...
AmericanIdiomsSlang1Sep2007
a dime a dozen adjective Definition: (idiomatic) so common as to be practically worthless. Example: Elvis impersonators are a dime a dozen Billy's ...
April62009AllDeptMtg
Good News Meeting Ground Rules PEOPLE * Aihua "Anna" Bian, Biostatistician I * Steven Chen, Assistant Professor * Mike Guo, Bioinformatics Systems Engineer ...
BasicSci
Basic Science Chairs * IT Infrastructure for Basic Sciences Main.FrankHarrell 04 Feb 2004
BeamerTips
Beamer Tips and Tricks Using * DocProcess has a few links to Beamer examples * Beamer Template is an example from Frank Harrell Handouts Frank's example ...
BiostatItGroup
Edit this topic to add a description to the BiostatItGroup
BiostatUsersGroup
Biostat Users Group * Set GROUP = ChangYu, ColeBeck, DalePlummer, DanielByrne, FrankHarrell, HeidiChen, SvetlanaEden, TatsukiKoyama, TebebGebretsadik, WilliamDupont ...
BonnieLaFleur
* Name: Bonnie LaFleur * Email: * Phone Number: * Comment: Research Interests * Statistical analysis * Permutation tests * Linear and nonlinear ...
CalendarComments
Calendar Comments Does the department's web calendar (http://biostat.mc.vanderbilt.edu/calendar) meet your needs? Do you use it? How could it be improved? If you ...
CancerBiostatWorkshop
2012 Center for Quantitative Sciences Workshop * Date: Third Friday of every month ( July, August, December) * Time: noon 1 pm (Lunch will be provided) ...
ColeAndWillFantasySportsApplication
Cole and Will Fantasy Sports Application Description An application that will facilitate fantasy sports drafts. Our first priority is football. It needs to import ...
ColeBeck
* Name: Cole Beck * Email: cole.beck #64;vumc.org * Phone: 3 6007 * Location: 2525 * Comment: You should call me if you need access to the Biostatistic ...
ColesPreferencesForm
*Name* Type Size Value Tooltip message PROJECTA text 15 Person taking on project A PROJECTB text 15 Person taking on project B LEADER text 15 Leader ...
ComputingClinic
Computing Clinic The Computing Clinic is currently on an extended hiatus (as of 12/2013) while the department's administration structure is being reorganized. We ...
ContinuingEducation
Biostatistics Seminars Attended I didn't record this unitl 12 Mar 2012 when informed to keep the attendance records. 1 14 Mar 2012: Theory and application of statistical ...
DataType
Project Form Documentation The type of data used in the study. This can be MicroArray or MassSpec. Name Type Tooltip message MassSpec option MicroArray ...
DeanAndBonniesFarewellParty
Dean and Bonnie's Farewell Party
DeanBillheimer
Dean Billheimer Contact Info * Name: Dean Billheimer * Email: * Phone: * Comment: "The essential distinction in the problem of inference is the distinction ...
ElizabethKoehler
Elizabeth Koehler, MS Contact Info * Email: e.koehler #64;vanderbilt.edu * Phone: 322 7193 Education * University of Washington MS in Biostatistics, ...
FacultyAccomplishments
Summary of Faculty Accomplishments Calendar Year Articles Published in Peer Reviewed Journals Books and Book Chapters Published Memberships on National Committees ...
FacultyStaff
Faculty and Staff of the Department of Biostatistics News Please visit Our People to view the actively maintained lists of our department members. This page presently ...
FantasyFootball
Fantasy Football What else did you think statisticians did for fun? Other than play ultimate. http://football.fantasysports.yahoo.com/league/biostat 2007 Results ...
FrequentlyAskedQuestionsFAQ
Frequently Asked Questions (FAQ) Working Remotely Procedures for using Zoom Related Topics * Facilities and Resources * Getting Started at Vanderbilt Biostatistics ...
GeneralWfccmDesign
General WFCCM Design * Wfccm Bug Reports Goals * Version 1 * Generate Scores. * Write basic graphs. * Version 2 * Add Permuatation ...
HddacAdminGroup
HDDAC Administrative Group A comma seperated list of TWiki names of those users who have write access to the HDDAC web * Set GROUP = WillGray, MingLi, BasharShakhtour ...
HddacGroup
HDDAC Group A comma seperated list of TWiki names of those uses who have write access in the HDDAC web * Set GROUP = TwikiAdmin, WillGray, YuShyr, MingLi, HeidiChen ...
HowToNameATwikiTopic
How to Name a Wiki Topic This topic is designed to help you choose a good name for your new wiki topic/page. It's easy and will make using the wiki easier for others ...
HowToSave10PercentAtCourtyardCafe
How To Save 10% at the Courtyard Cafe The Courtyard Cafe gives a 10% VUMC employee discount when you use your Commodore Card (id badge) to pay. Here's how to add ...
HowtoBuildHomepage
A Checklist to Your Personal Homepage 1. Photo (refer to "How to Add Your Picture Onto the Homepage in 4 Easy Steps") 1. Contact information: address, phone ...
HuimingLi
* Name: HuimingLi * Email: * Phone Number: 3438608 * Comment: Personal Preferences (details in .TWikiVariables) * Horizontal size of text edit box: ...
ImproveTurnAroundTime
Templates for Grant Proposals * Statistical Components for Grant Proposals * Study Design * Sample Size Calculation * Statistical Method Templates for ...
IndividualEffortCertificationMeetings
Individual Effort Certification Meetings will last ten minutes each. Name September 29 October27 November November 10:30 ...
IntramuralFrisbee
Ultimate Frisbee Intramurals Yay frisbee! If you're interested in participating, please e mail Cole Beck or Jeremy Stephens. About Ultimate Ultimate frisbee is a ...
IntramuralSports
Biostatistics Intramural Sports This is the portal to the various Vanderbilt intramurals we've participated in. Here's a link to the official intramural calendar ...
JoAnnAlvarez
JoAnn Alvarez, MA Biostatistician III E mail: joannmalvarez #64;gmail.com Office: 490 Preston Research Building My CV and resume (word file) Interests ...
July2010AllDeptMtg
July 13, 2010 (MRBIII, Room 1220 2:00PM) Good News * BINGO! * Winners Marcia and Alex * Linda returning home * Cindy Chen's R21 receives a very high ...
JumpStartForNewBiostatisticians
Welcome to the Department of Biostatistics! Here are some useful resources for you to learn about R, Sweave/LaTeX, longitudinal data analysis, survival analysis and ...
KubuntuNotes
Kubuntu Notes Gutsy Gibbon Fuzzy Fonts After upgrading to gutsy, fonts might appear a little fuzzy. To fix this, go to System Settings Appearance Fonts and ...
LatestRFunctions
How to Obtain Updates to Individual Functions in R Packages Between Releases This page shows you how to read in source code to override functions in a package. The ...
LinuxAndSecurity
Linux Workshop: General Linux Information and Security Tips March 26, 2008 Linux Information Links for Further Reading * Linux.com and Linux.org. * Linux Today ...
LinuxWorkshopRProgramingTipsAndGotchas
R Programing Gotchas R Gotchas R has several 'features' that can trip up those who are not aware of them. Non Value Values. R contains several values are specially ...
MaMsAdditionalTools
Additional Tools * InfoLog.exe: Info Score generator * WGALog.exe: WGA Score generator * sam2003 07 07_v1.21.zip: SAM excel score generator * msjavx86 ...
MassionMDA
Massion MDA Mouse Study * Start Date: 31 August 2004 * Finish Date: 20 September 2004 * Research Drive Directory: /Massion/040831/ * Data Type: MassSpec ...
MassionSerum518
Massion Serum 518 Study * Start Date: 11 Nov 2004 * Research Drive Directory: /Massion/041111_serum 518/ * Data Type: MassSpec * Notes: * Status: ...
MassionSerumMaldiCelebrexTaxotere
Massion Serum MALDI Celebrex Taxotere Study * Start Date: 30 Aug 2004 * Research Drive Directory: /Massion/040830/ * data (data.txt, data_log10.txt) is ...
MicroArrayMassSpecProjectForm
Form definition for MicroArrayMassSpec projects Name Type Size Values Tooltip message ProjectClassification select 1 Project type StudyName ...
MicroArrayMassSpecProjectTemplate
Notes Analysis Requests 1 question 1 question Status 1 0% 1 0% Output Change Log * 20 Sep 2004 * change
ModdingMozilla
Linux Workshop Modding Mozilla Themes extensions can enhance Firefox and Thunderbird June 29, 2005 * The web site for Firefox and Thunderbird extensions is ...
NewHireProcedures
New Hire Procedures * Information Technology Procedures for New Employees * Administrative Procedures for New Employees * Welcome to Vanderbilt 30 Day Survey ...
NimishGautam
* Name: Nimish Gautam * Email: nimish.gautam #64;vanderbilt.edu * Phone Number: * Comment: Personal Preferences (details in .TWikiVariables) * Horizontal ...
OurPeople
Our People Faculty (Full and Associate Professors) %Main.PhotoList.YUSHYRINFO% %Main.PhotoList.FRANKHARRELLINFO% %Main.PhotoList.WILLIAMDUPONTINFO% %Main ...
PotLuck2006RSVP
Potluck Party 2006 Thing To Bring Along 1 Beverages 1 Main Dishes 1 Side Dishes 1 Desserts RSVP Employee's Name Number To Attend To Bring Along ...
PotLuckFeb2007ToBring
Biostatistics Potluck Party Monday, February 12 at 11:00 AM (Lunch); PRB 898 A B General Rules * For Biostat. faculty and staff only * Things don't need ...
Project20050512212939
Tester Notes Analysis Requests 1 question 1 question Status 1 0% 1 0% Output Change Log: * date: 20 Sep 2004 * change
Project20050517112309
Massion Serum Notes * Serum data (A 291) w/ ProTS software preprocessing by JeremyNorris's group Analysis Requests 1 Normal vs Cancer * top57 ...
Project20050616150308
Lung Spores Take Notes Analysis Requests 1 question 1 question Status 1 0% 1 0% Output Change Log * 20 Sep 2004 * change
ProjectClassification
Project Form Documentation Project classification. Name Type Tooltip message MaMsProject option Ma/Ms Project Obsolete option Use this to hide ...
ProjectStatus
Project Form Documentation The status of the project as a whole. Name Type Tooltip message New option Active option Complete option
RClinicHelpfulRCode4
How to write your own functions and good R programing techniques Good R Programing Techniques R is quite different from regular programing languages in the way that ...
RGraphicsDotplot
Making Dot Charts in R Rachel Hayes brought a problem to R Clinic on 23Oct08. The Hmisc Dotplot function can produce multi panel dot charts with error bars while ...
RVim
R and VIM Syntax Highlighting and Indenting I modified the existing R vim syntax file, and created a vim R indent file since R's indention in vim was broken. Below ...
RecommendedReading
Recommended Reading In Reverse Chronological Order by Date of Publication Authors Title Journal Issue Page Comments Jones RH Bayesian information ...
RedcapApiExportR
An R function for redcap exports through the API Here is an R function that exports data from redcap through the API within R. This function, along with new options ...
RenamingFilesInVisualSourceSafe
Renaming files in Microsoft VSS This may sound tricky, but it's actually rather simple. The reason behind this method is to preserve the file history. It helps to ...
SchoolOfMedicineCommittees
School of Medicine Committees * Basic Science Chairs * Our representative to the School's Faculty Advisory Committee: Robert Greevy (2007 2009) following Patrick ...
ScrabbleServerRegistration
Scrabble Server Registration The server's current version is 1.6.2. Registration and Login Steps * Start PyScrabble * Click Find Public Servers * Click Add ...
SharedResourceGroup
Shared Resource Group * Set GROUP = BasharShakhtour, HeidiChen, TatsukiKoyama, WillGray, YuShyr, MingLi, FeiYe, DanAyers, DavidBiagi * Set ALLOWTOPICCHANGE ...
SharedResourceSvnSwitch
Using Subversion for Source Control Steps * Confirm nightly backup * Repositories on Biostatdebian * Configure SVN service * Test migration vss2svn on ...
SoftballPictures2009
Loading image. Please wait Intramural Softball May 21, 2009 Team Photo (L R) Nate, Will, Cole (L R) Cathy, Umpire, Jeremy, Patrick (L R) Will, Kylie, Jeremy, Nate ...
SoftballTeamShirts
Softball team shirt orders are due no later than August 26 at 4 pm. Please contact Seth with general questions regarding shirt orders, and contact Cole or Will with ...
SteveMeurerMtgItineraryJune
Steve Meurer, PhD, MBA, MHS Senior Vice President, Comparative Data Informatics http://biostat.mc.vanderbilt.edu/SteveMeurerJune1 Wednesday, June 1, 2011 TIME ...
SweaveConvert
Converting Documents Produced by Sweave and knitr Converting from LaTeX to html The recommended format for statistical reports to send to collaborators is pdf produced ...
SystemScriptHowto
How to Define Your Own System Command Scripts The following uses the small, handy pico editor. Suppose that the command script you want to create is called zzz. ...
TWikiUsers
List of Vanderbilt Biostatistics Wiki users To edit pages on this site, you must have a registered user name and password. You do not need to register if you just ...
TatsukiRcode
R code for tplot, kmplot and other functions. * RFunctions1.R: RFunctions1.R R code for other miscellaneous functions. * RFunctions2.R: RFunctions2.R R code ...
TwikiAccessDiscussion
Twiki Access Discussion Problem As part of forming the High Dimensional Data Analysis Core, we set up the HDDAC web on the twiki. We want the data to be secure, ...
TwikiFirefoxExtensions
TWiki Firefox Add ons These are some add ons to help with using the TWiki. Navigation TWiki Browser Plugins has some Firefox search plugins for searching and ...
TwoStageIntroduction
Making Inference from a Simon's Two stage Design in Phase II Clinical Trials by Tatsuki Koyama * New page TwoStageInference
VandyGoGreen
Vanderbilt has established an Office of Sustainability and Environmental Management; their web site SustainVU contains valuable information about conserving important ...
WebAppRegistry
Web Application Registry Members of the Department of Biostatistics and the Center for Quantitative Sciences have developed or participated in the development of web ...
WebStatistics2004
Statistics for Main Web in 2004 Current Web Statistics Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
WebStatistics2005
Statistics for Main Web in 2005 Current Web Statistics Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
WebStatistics2007
Statistics for Main Web in 2007 Current Web Statistics Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
WebStatistics2008
Statistics for Main Web (2008) Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads ...
Wfccm2CommandLineDownload
Command Line Wfccm * Runs under Mono for Linux support * Incorporates basic Wfccm functionality
Wfccm2Guide
WFCCM 2 How To Step by step Step 1: Loading the Data and Information Sets * Go to "File Add a Data Set" to add the given data * The name of the Data ...
Wfccm2PublicDownload
* Version 1.0.00 dd mmm yyyy: Public release. Score generation and distance complete. For instructions, please refer to the guide. If you can not run the project, ...
WfccmAddGroupingsCriteriaManagers
Add DataGroupings and CriteriaManagers DataGroupings Working on a large project and having to create the same 6 groupings several times (incuding creating columns ...
WfccmAlgorithmFDR
False Discovery Rate Algorithm Calculate adjusted p values using False Discovery Rate Controlling Procedures. FDR Algorithm predefined values: subSize of data ...
WfccmAlgorithmFisher
Fisher Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There ...
WfccmAlgorithmHu
Hu Algorithm function 1 : log likelihood to estimate logmu * f(logmu) = %$\sum(\frac{1}{2}*logsigma2 \frac{(X exp(logmu))^2}{2*exp(logsigma2)})$% * logsigma2 ...
WfccmAlgorithmInfo
Info Algorithm Performed on an ordered (ascending) set of numbers and labels of size N. There must be only 2 unique labels (Label 1 and label 2). Seperate the list ...
WfccmAlgorithmLikelihoodRatio
Likelihood Ratio Algorithm Suppose that we have data from stratum 0 and stratum 1. The test statistic is computed as : %$Z = 2Nlog(\frac{T}{N}) 2\sum N_jlog(\frac ...
WfccmAlgorithmLogRankWilcoxon
Log Rank and Wilcoxon Algorithm These tests are for comparison of two or more strata of survival data. Suppose that we have data from stratum 0 and stratum 1. Denote ...
WfccmAlgorithmPermutationTTest
Permutation TTest Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must ...
WfccmAlgorithmSAM
SAM Algorithm The data is %$x_{ij}$%, i = 1, 2, ... p genes, j = 1, 2, ... n samples, and response data %$y_j$%, j = 1,2, ... n (%$y_j$% may be a vector). Generic ...
WfccmAlgorithmTTest
TTest Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There ...
WfccmAlgorithmWGA
WGA Algorithm WGA = \begin{displaymath} \frac{d_b}{k_1d_{1} k_2d_{2} \alpha} \end{displaymath} * description of letters * %$n_i$% is the total number of ...
WfccmAlgorithmWilcoxon
Wilcoxon Algorithm Performed on a set of numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There can also be ...
WfccmBugReport20050516140742
No Score Summary The score summary was only giving the max values for SAM, WGA, and Hu instead of a table of possible cutoffs. The problem was occuring for a DataSet ...
WfccmBugReport20050810132022
Extra score summary row Summary.ScoreSummary sometimes puts a duplicate row at the very bottom. For example, WGA 0.01 Follow up on 17 Mar 2006 I haven't observed ...
WfccmBugReport20050810132327
Bad testing dataset information added training data set information while it's supposed to add testing data set information, it affected Summarypercentage class and ...
WfccmBugReport20050810132742
Bad path in state mainTree node showed training set folder name after running a testing set, it caused part of saved state couldn't work anymore since it can not find ...
WfccmBugReport20050825093746
Incorrect BallGraph Title The ballgraph was automatically generated when I clicked run 50 on a top200 graph. The ballgraph's title said it was run 100. It's has ...
WfccmBugReport20050829104513
No Ballgraph Generated When I click on model 1 of a cutoff, the ball graph is not generated. Is is trying to compensate for topN? If so, this is not a good solution ...
WfccmBugReport20050902164819
Cannot Save Cluster Unhandled exception 'incorrect parameter used' when trying to save a cluster of the entire dataset (not filtered by a winner list). F:\Lu\050326HJ ...
WfccmBugReport20050913122218
Cannot load Unix format datafile For some reason, MemoryMapDataSet is not correctly determining that Unix and Mac file formats use a single byte for newlines (CR or ...
WfccmBugReport20050922160446
Invalid specified cast This error occurs when trying to run Cross Validation Distance. The illegal cast occurs during the creation/setup of the SummaryPercentages ...
WfccmBugReport20050928132656
Object reference not set When trying to generate a ball graph for cross validation distance topN results, an unhandled exception occured. Object reference not set ...
WfccmBugReport20051010102418
Missclassified Patients 50% Threshold The graph for missed columns/patients in the testing data does not appear when the testing data classification is lower than ...
WfccmBugReport20051024105057
Cannot disply VizSpec when more than one averaged data loaded Describe the bug here.
WfccmBugReport20051024110037
Incorrect Double Progress bar when more than one distance run submitted, the outter progress bar shows "0 of n" or "1 of n ", it doens't show " n 2 of n" or "n 1 of ...
WfccmBugReport20051024140341
Incorrect VizSpectra Zoom function error occurs when continue use zoom function in vizSpec (normally afterusing 5 6 times zoom function); Grab function doesn't have ...
WfccmBugReport20051031161207
p values cannot be compeletely displayed when p values less than 0.000001, it shows 0.00000 in the information box.
WfccmBugReport20051101113226
Distance Permutation Number Not Loading Entering the distance p value permutation number works correctly, but it is not showing up when selecting the criteria. This ...
WfccmBugReport20051102144703
cannot show ROC based on cutoffs * no ROC curve shows up while the node shows up
WfccmBugReport20051130095245
Non delete I deleted groupings and re added them so I could re run the statistical tests. I saved state and re loaded. Then, there were multiple (2 or 3) score nodes ...
WfccmBugReport20060320132452
The Info Score There are two datasets. One is the whole dataset which includes all the samples, and the other only includes the samples I need. I use the same grouping ...
WfccmBugReport20060320133551
ROC Can not generate the ROC curve. Needs more information. Version number is incorrect.
WfccmBugReport20060519100152
Cannot write missed column report Steps to Reproduce Get the data from Bashar and run the same comparisons. Expected Behavior Observed Behavior Application threw ...
WfccmBugReport20060714084422
Panel not updated on new grouping created Steps to Reproduce Create a new grouping. Expected Behavior The grouping panel should updated to reflected the saved grouping ...
WfccmBugReport20060731104352
Error saving winner lists for cross validation Steps to Reproduce Run cutoff or topN cross validation distance. Expected Behavior Observed Behavior The first model ...
WfccmBugReport20060801125208
Duplicate distance results Steps to Reproduce Run distance, save state, close WFCCM, and reload. Expected Behavior Observed Behavior On loading a saved state, there ...
WfccmBugReportForm
Wfccm Bug Report Form Definition Name Type Size Values Tooltip message BugClassification select 1 WfccmBug, Obsolete Wfccm Bug BugStatus select 1 Outstanding ...
WfccmBugReportTemplate
Steps to Reproduce Expected Behavior Observed Behavior
WfccmBugReports
Bug Reports Create Bug Report Bug Name Version User Date Outstanding View/edit Name Version Reported Date ** ...
WfccmChartPanel
ChartPanel Public Methods * saveImage(String imgName) saves image of the chart (as a PNG file) to the given image name * setDimensions(float top, bottom, ...
WfccmClassDescriptions
Interface descriptions * IDataSet Interface for datasets. Class descriptions * DataContainer Parent class for the data classes * InformationSet ...
WfccmClassTemplate
ClassName Public Methods Properties Protected Methods Private Methods Virtual Methods Protected Members Exceptions Rationale Remarks
WfccmClusterNode
ClusterNode Enumeration NodeType * Node * Gene * Array Static (Class) Methods * ClusterNode Compare3(ClusterNode, ClusterNode, ClusterNode, bool) ...
WfccmClusterSummary
ClusterSummary NameRank Class * name * rank Public Methods * Load(string) Loads the given CDT file * string GetArryNameByRank(name, rank) given ...
WfccmCombinationManager
CombinationManager Public Methods * SetBases(ArrayList of int) Sets the sizes of the bases. * Arraylist GetCombination(int) Returns the 0 base indices that ...
WfccmCommandLineMethod
Console Wfccm Command line aspect of Wfccm. Limited capability extended. Todo * Add support for Shuo's preprocessed data log transformation not applicable ...
WfccmCommentingGuidelines
Commenting Guidelines * Add class/function header at time of creation * Use summary to describe a function/class. * Use value to describe a property ...
WfccmCriteria
Criteria Public Members * Property Name * Property Operator * Property Value * Property IgnoreNumPass Protected * string name Name of the ...
WfccmCriteriaManager
CriteriaManager Public Methods * CriteriaManager(CriteriaManager) The copy constructor. * Remove(string, string, double) Removes a score name, operator ...
WfccmCriteriaManagerPanel
CriteriaManagerPanel Public Methods * loadCM(CriteriaManager, ArrayList, bool) Takes the CriteriaManager to load, a list of score names, and whether or not the ...
WfccmCriteriaManagerWarning
CriteriaManagerWarning Confirms changing the CriteriaManager type on the CriteriaManagerPanel because all criteria and the STD function are removed.
WfccmCriteriaSet
CriteriaSet Public Methods * Property Pass * Property NumPass The number of rows that passed the evaluation. If IgnoreNumPass then don't count. * SetColumnValue ...
WfccmCrossValidation
Cross Validation TODO * Refactor Distance calculation. * Swap loops so the cross validation (kFold) loop is inside the TopNManager (c) loop. * ...
WfccmCutoffManager
CutoffManager Parent: CriteriaManager Public Methods * CutoffManager(CutoffManager) The copy constructor. * Add(string, string, double) Adds a score name ...
WfccmDataContainer
DataContainer Public Methods * DataContainer(DataContainer) Copy constructer. * AddColumn(string) Appends a new column of data, sets the name, and returns ...
WfccmDataGrouping
DataGrouping Public Methods * DataGrouping(DataGrouping) Copy constructor. * Add(string, string) Adds a Column by name and sets group descriptor (defaults ...
WfccmDataGroupingPanel
DataGroupingPanel Public Methods * loadDG(DataSetInfo, DataGrouping, bool, bool) Takes the data information, the grouping to load, and whether the grouping is ...
WfccmDataSet
DataSet Parent: DataContainer, Interface: IDataSet Public Methods * DataSet(DataSet) Copy Constructor overload that handles the name list. * SetDataPoint ...
WfccmDataSetPanel
DataSetPanel Public Methods * LoadDataSetPanel(DataSetInfo) loads the DataSet contained within the DataSetInfo object. If an InformationSet has also been assigned ...
WfccmDataStructureRefactor
This has been set aside for now, being replaced by memory mapped files. Temporary memory saving solution until C# 2.0 is officially released. Since an object takes ...
WfccmDistanceReport
DistanceReport Static Methods * WriteMissedColumn(ArrayList, string, bool, double) Will first filter distanceResults for runs where overall percent correct ...
WfccmDistanceResult
DistanceResult Public Members * FilteredScores List of ids, numPass and the modifiers. * CriteriaSet criteria * DistanceOutput train * DistanceOutput ...
WfccmExceptionCodes
* Copy and Paste will work * WfccmExceptionCodes Creation error "\n Failure when trying to create " this.GetType().ToString() " `" this.name "'!" Add row ...
WfccmExpression
Expression Public Methods * Expression(string) Creation constructor. Sets function to the passed string, checks the validity of the function and converts to ...
WfccmFilteredScore
FilteredScore Parent: Score Public Methods * FilteredScore(Score, CriteriaSet) Filters a score according to the criteria set. Creates the numPass column. ...
WfccmFunctionalityRequestsAndChanges
Functionality Requests * Change T test p value calculation from equal variance to unequal variance. * Eisen like data overview with sortable columns and groupings ...
WfccmGenericDataStructures
C# 2.0 (.NET 2005 Whidbey) supports generics * Change DataContainer to DataContainer T * Replace ArrayList with Generic.List T * Replace SortedList ...
WfccmIDataSet
IDataSet Public Methods * GetDataPoint(int, int) * GetColumnName(int) * GetColIndexFromName(string) * GetRowId(int) * GetRowIndexFromId(int) * GetRowName ...
WfccmInformationSet
InformationSet Parent: DataContainer Public * SetDataPoint(int, int, string) Set the data at that point. * GetDataPoint(int, int) Gets the data at that ...
WfccmLargeDataSetCapability
Large Data Set Capability Detailed Time Line and Tasks Large DataSet Implementaiton Apr18 May 06 3 weeks 1. Implement objects. 1. Build the interface. ...
WfccmLargeDataSetSubClassProsCons
Large DataSet SubClass Pros and Cons Description For large dataset capabilities, we might need to make the read only MemoryMapDataSet a subclass of DataSet. Pros ...
WfccmMemoryMapDataSet
MemoryMapDataSet Interface: IDataSet Public Methods * MemoryMapDataSet(string) Constructor that takes the path/file name. * MemoryMapDataSet(string, int) ...
WfccmMissedValues
MissedValues Note: This class's structure is dependent entirely on DistanceReport.WriteMissedColumn() function Public Members * highlightRuns Arraylist of highlighted ...
WfccmNetwork
Network Public Methods * Network(IPAddress, int) Constructor for starting a connection. * Network(string, int) Constructor for starting a connection. ...
WfccmNetworkListener
NetworkListener Public Methods * NetworkListener(int) The constructor. * Start() Starts listening for incoming connections. * Stop() Stops listening ...
WfccmNotes
Meeting Notes Nov 3 * Tasks * First stage, build database and interfaces * Haojie, Huiming, Joe * 15 Dec 2005 April 5 * Slides ...
WfccmOptionData
OptionData Public Methods * OptionData() * OptionData(string) * Copy() * Load(string) * Save(string) Properties * AutoLoadLog * AutoLoadInfo ...
WfccmOptions
Options in Wfccm2 Instead of forcing the load and save dialogs, we could have import/export options with buttons or a menu. Are we going to only use the flat file ...
WfccmPartitionedDataSet
PartitionedDataSet Public Methods * PartitionedDataSet(string) Constructor that takes the path to the DataSet. * PartitionedDataSet(string, int) Constructor ...
WfccmPrePostHowto
WFCCM Pre Post Guide This is a guide for running pre post analysis in WFCCM. For a pre post analysis, there needs to be a pre treatment and post treatment sample for ...
WfccmProjectData
ProjectData Public * Collection of DataSetInfo * string working directory * class DataSetInfo * path for data set * path for score set ...
WfccmRequirements
Requirements Statement The software to be designed will control the generation of scores to be used is the distance analysis of genes and proteins via WFCCM. The program ...
WfccmRfunctions
Rfunctions Public Methods * Average(ArrayList) Returns the mean. * StDev(ArrayList, double) Returns the standard deviation. * Var(ArrayList) Returns ...
WfccmScoreExpression
ScoreExpression Parent: Score Public Methods * GenerateScores(DataSet, DataGrouping) defaults to ignore zeroes * GenerateScores(DataSet, DataGrouping, bool ...
WfccmScoreHu
ScoreHu Public Methods * ScoreHu() Default Constructor. * ScoreHu(ScoreHu) Copy Constructor. * ScoreHu(string) Loads the score from a file. ...
WfccmScoreSam
ScoreSam Parent: Score Public Methods * ScoreSam() the default constructor. * ScoreSam(ScoreSam) copy constructor. * ScoreSam(string) Constructors ...
WfccmScoreTTest
ScoreTTest Parent: Score Public Methods * ScoreTTest() the default constructor. * ScoreTTest(ScoreTTest) copy constructor. * ScoreTTest(string) ...
WfccmSourceFileStructureRefactor
Vicc.Biostat Wfccm.Forms * CriteriaManagerPanel * CriteriaManagerWarning * DataGroupingPanel * DataSetPanel * DataSetView * DistancePanel * InformationPane ...
WfccmSummaryModule
Summary Public Methods * ScoreSummary(ArrayList) Returns an InformationSet that summarizes all of the Scores given. * ScoreSummary(Score, ...) ScoreSummary ...
WfccmSummaryPanel
SummaryPanel Public Methods * SummaryPanel() Default constructor * SummaryPanel(SummaryPercentages) create a new Summary panel with the given percentages ...
WfccmSummaryPercentages
SummaryPercentages Public Members * ArrayList Grp1 Grp2 Pcts Train Test Percentages * ArrayList Train Test Pcts Percentages for training or testing ...
WfccmTestingGuidelines
Please put your feedback on this system. I think that this will work, but I am open to better solutions. Jeremy. At this point in time, use the console tester to write ...
WfccmTopnManager
TopNManager Parent: CriteriaManager Public Members * TopNManager(TopNManager) The copy constructor. * Add(string, string, double) Adds a score name, operator ...
WikiWalkthrough
Foswiki or TWiki? Foswiki is a fork of the TWiki software. If you want to know why the fork was created, read this. It was in our best interest to switch because ...
WillGrayLeftBar
Customise this topic; samples and ideas available at TWiki:TWiki.WebLeftBarCookbook. * * WfccmBugReports * WfccmDistributedComputing * MicroArrayMassSpec ...
WillGrayNotifyList
WillGrayNotifyList This topic defines the e mail notifications I receive when certain topics change. * Set ALLOWTOPICCHANGE = WillGray Topic immediate notifications ...
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