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Function Index.Time.Series [Ecdat v0.3-1]
keywords
documentation
title
Time Series
description
annual Klein : Klein's Model I LT : Dollar Sterling Exchange Rate Longley : The Longley Data ManufCost : Manufacturing Costs Mpyr : Money, National Product and Interest Rate PE : Price and Earnings Index Solow : Solow's Technological Change Data daily CRSPday : Daily Returns from the CRSP Database Garch : Daily Observations on Exchange Rates of the US Dollar Against Other Currencies SP500 : Returns on Standard \& Poor's 500 Index four--weekly Icecream : Ice Cream Consumption monthly CRSPmon : Monthly Returns from the CRSP Database Capm : Stock Market Data Forward : Exchange Rates of US Dollar Against Other Currencies Irates : Monthly Interest Rates Mishkin : Inflation and Interest Rates Orange : The Orange Juice Data Set PPP : Exchange Rates and Price Indices for France and Italy Pricing : Returns of Size-based Portfolios StrikeNb : Number of Strikes in Us Manufacturing quarterly Consumption : Quarterly Data on Consumption and Expenditure Hstarts : Housing Starts IncomeUK : Seasonally Unadjusted Quarterly Data on Disposable Income and Expenditure MW : Growth of Disposable Income and Treasury Bill Rate Macrodat : Macroeconomic Time Series for the United States Money : Money, GDP and Interest Rate in Canada MoneyUS : Macroeconomic Series for the United States Tbrate : Interest Rate, GDP and Inflation weekly DM : DM Dollar Exchange Rate Pound : Pound-dollar Exchange Rate Yen : Yen-dollar Exchange Rate
Function Index.Econometrics [Ecdat v0.3-1]
keywords
documentation
title
Econometric fields
description
binomial model Benefits : Unemployment of Blue Collar Workers Hmda : The Boston HMDA Data Set Mroz : Labor Supply Data Participation : Labor Force Participation Train : Stated Preferences for Train Traveling censored and truncated model Fair : Extramarital Affairs Data HI : Health Insurance and Hours Worked By Wives Mofa : International Expansion of U.S. Mofa's (majority--owned Foreign Affiliates in Fire (finance, Insurance and Real Estate) Tobacco : Households Tobacco Budget Share Workinghours : Wife Working Hours count data Accident : Ship Accidents Bids : Bids Received By U.S. Firms Doctor : Number of Doctor Visits DoctorAUS : Doctor Visits in Australia DoctorContacts : Contacts With Medical Doctor OFP : Visits to Physician Office PatentsHGH : Dynamic Relation Between Patents and R\&D PatentsRD : Patents, R\&D and Technological Spillovers for a Panel of Firms Somerville : Visits to Lake Somerville StrikeNb : Number of Strikes in Us Manufacturing duration model Oil : Oil Investment Strike : Strike Duration Data StrikeDur : Strikes Duration UnempDur : Unemployment Duration Unemployment : Unemployment Duration multinomial model Car : Stated Preferences for Car Choice Catsup : Choice of Brand for Catsup Cracker : Choice of Brand for Crakers Fishing : Choice of Fishing Mode HC : Heating and Cooling System Choice in Newly Built Houses in California Heating : Heating System Choice in California Houses Ketchup : Choice of Brand for Ketchup Mode : Mode Choice ModeChoice : Data to Study Travel Mode Choice Tuna : Choice of Brand for Tuna Yogurt : Choice of Brand for Yogurts ordered model Kakadu : Willingness to Pay for the Preservation of the Kakadu National Park Mathlevel : Level of Calculus Attained for Students Taking Advanced Micro--economics NaturalPark : Willingness to Pay for the Preservation of the Alentejo Natural Park panel Airline : Cost for U.S. Airlines Cigar : Cigarette Consumption Cigarette : The Cigarette Consumption Panel Data Set Crime : Crime in North Carolina Fatality : Drunk Driving Laws and Traffic Deaths Gasoline : Gasoline Consumption Grunfeld : Grunfeld Investment Data LaborSupply : Wages and Hours Worked Males : Wages and Education of Young Males MunExp : Municipal Expenditure Data Produc : Us States Production SumHes : The Penn Table Wages : Panel Datas of Individual Wages system of equations BudgetItaly : Budget Shares for Italian Households BudgetUK : Budget Shares of British Households Electricity : Cost Function for Electricity Producers Klein : Klein's Model I ManufCost : Manufacturing Costs Nerlove : Cost Function for Electricity Producers, 1955 University : Provision of University Teaching and Research time--series CRSPday : Daily Returns from the CRSP Database CRSPmon : Monthly Returns from the CRSP Database Capm : Stock Market Data Consumption : Quarterly Data on Consumption and Expenditure DM : DM Dollar Exchange Rate Forward : Exchange Rates of US Dollar Against Other Currencies Garch : Daily Observations on Exchange Rates of the US Dollar Against Other Currencies Hstarts : Housing Starts Icecream : Ice Cream Consumption IncomeUK : Seasonally Unadjusted Quarterly Data on Disposable Income and Expenditure Irates : Monthly Interest Rates LT : Dollar Sterling Exchange Rate MW : Growth of Disposable Income and Treasury Bill Rate Macrodat : Macroeconomic Time Series for the United States Mishkin : Inflation and Interest Rates MoneyUS : Macroeconomic Series for the United States Mpyr : Money, National Product and Interest Rate Orange : The Orange Juice Data Set PE : Price and Earnings Index PPP : Exchange Rates and Price Indices for France and Italy Pound : Pound-dollar Exchange Rate Pricing : Returns of Size-based Portfolios Solow : Solow's Technological Change Data Tbrate : Interest Rate, GDP and Inflation Yen : Yen-dollar Exchange Rate
Function Index.Economics [Ecdat v0.3-1]
keywords
documentation
title
Economic fields
description
consumer behavior BudgetFood : Budget Share of Food for Spanish Households BudgetItaly : Budget Shares for Italian Households BudgetUK : Budget Shares of British Households Car : Stated Preferences for Car Choice Cigar : Cigarette Consumption Cigarette : The Cigarette Consumption Panel Data Set Doctor : Number of Doctor Visits Fishing : Choice of Fishing Mode Gasoline : Gasoline Consumption HC : Heating and Cooling System Choice in Newly Built Houses in California Heating : Heating System Choice in California Houses Icecream : Ice Cream Consumption Mode : Mode Choice ModeChoice : Data to Study Travel Mode Choice Somerville : Visits to Lake Somerville Tobacco : Households Tobacco Budget Share Train : Stated Preferences for Train Traveling economics of education Caschool : The California Test Score Data Set MCAS : The Massachusetts Test Score Data Set Mathlevel : Level of Calculus Attained for Students Taking Advanced Micro--economics Star : Effects on Learning of Small Class Sizes environmental economics Airq : Air Quality for Californian Metropolitan Areas Kakadu : Willingness to Pay for the Preservation of the Kakadu National Park NaturalPark : Willingness to Pay for the Preservation of the Alentejo Natural Park finance CRSPday : Daily Returns from the CRSP Database CRSPmon : Monthly Returns from the CRSP Database Capm : Stock Market Data DM : DM Dollar Exchange Rate Forward : Exchange Rates of US Dollar Against Other Currencies Garch : Daily Observations on Exchange Rates of the US Dollar Against Other Currencies Irates : Monthly Interest Rates LT : Dollar Sterling Exchange Rate PPP : Exchange Rates and Price Indices for France and Italy Pound : Pound-dollar Exchange Rate Pricing : Returns of Size-based Portfolios Yen : Yen-dollar Exchange Rate game theory FriendFoe : Data from the Television Game Show Friend Or Foe ? health economics DoctorAUS : Doctor Visits in Australia DoctorContacts : Contacts With Medical Doctor MedExp : Structure of Demand for Medical Care OFP : Visits to Physician Office VietNamH : Medical Expenses in Viet--nam (household Level) VietNamI : Medical Expenses in Viet--nam (individual Level) hedonic prices Computers : Prices of Personal Computers Diamond : Pricing the C's of Diamond Stones Hedonic : Hedonic Prices of Census Tracts in Boston Housing : Sales Prices of Houses in the City of Windsor Journals : Economic Journals Dat Set labor economics Benefits : Unemployment of Blue Collar Workers Bwages : Wages in Belgium CPSch3 : Earnings from the Current Population Survey Earnings : Earnings for Three Age Groups Griliches : Wage Datas HI : Health Insurance and Hours Worked By Wives LaborSupply : Wages and Hours Worked Labour : Belgian Firms Males : Wages and Education of Young Males Mroz : Labor Supply Data PSID : Panel Survey of Income Dynamics Participation : Labor Force Participation RetSchool : Return to Schooling Schooling : Wages and Schooling Strike : Strike Duration Data StrikeDur : Strikes Duration StrikeNb : Number of Strikes in Us Manufacturing Treatment : Evaluating Treatment Effect of Training on Earnings UnempDur : Unemployment Duration Unemployment : Unemployment Duration Wages : Panel Datas of Individual Wages Wages1 : Wages, Experience and Schooling Workinghours : Wife Working Hours macroeconomics Consumption : Quarterly Data on Consumption and Expenditure Hstarts : Housing Starts IncomeUK : Seasonally Unadjusted Quarterly Data on Disposable Income and Expenditure Klein : Klein's Model I Longley : The Longley Data MW : Growth of Disposable Income and Treasury Bill Rate Macrodat : Macroeconomic Time Series for the United States Mishkin : Inflation and Interest Rates Money : Money, GDP and Interest Rate in Canada MoneyUS : Macroeconomic Series for the United States Mpyr : Money, National Product and Interest Rate PE : Price and Earnings Index Produc : Us States Production Solow : Solow's Technological Change Data SumHes : The Penn Table Tbrate : Interest Rate, GDP and Inflation marketing Catsup : Choice of Brand for Catsup Cracker : Choice of Brand for Crakers Ketchup : Choice of Brand for Ketchup Tuna : Choice of Brand for Tuna Yogurt : Choice of Brand for Yogurts producer behavior Accident : Ship Accidents Airline : Cost for U.S. Airlines Bids : Bids Received By U.S. Firms Clothing : Sales Data of Men's Fashion Stores Electricity : Cost Function for Electricity Producers Grunfeld : Grunfeld Investment Data Hmda : The Boston HMDA Data Set ManufCost : Manufacturing Costs Metal : Production for SIC 33 Mofa : International Expansion of U.S. Mofa's (majority--owned Foreign Affiliates in Fire (finance, Insurance and Real Estate) Nerlove : Cost Function for Electricity Producers, 1955 Oil : Oil Investment Orange : The Orange Juice Data Set PatentsHGH : Dynamic Relation Between Patents and R\&D PatentsRD : Patents, R\&D and Technological Spillovers for a Panel of Firms TranspEq : Statewide Data on Transportation Equipment Manufacturing University : Provision of University Teaching and Research socio--economics Crime : Crime in North Carolina Fair : Extramarital Affairs Data Fatality : Drunk Driving Laws and Traffic Deaths
Function Index.Source [Ecdat v0.3-1]
keywords
documentation
title
Source
description
Journal of Applied Econometrics data archive : http://qed.econ.queensu.ca/jae/ Bids : Bids Received By U.S. Firms BudgetFood : Budget Share of Food for Spanish Households BudgetItaly : Budget Shares for Italian Households BudgetUK : Budget Shares of British Households Car : Stated Preferences for Car Choice Computers : Prices of Personal Computers Crime : Crime in North Carolina Doctor : Number of Doctor Visits Earnings : Earnings for Three Age Groups HI : Health Insurance and Hours Worked By Wives Housing : Sales Prices of Houses in the City of Windsor Males : Wages and Education of Young Males Mathlevel : Level of Calculus Attained for Students Taking Advanced Micro--economics MoneyUS : Macroeconomic Series for the United States MunExp : Municipal Expenditure Data OFP : Visits to Physician Office Oil : Oil Investment Participation : Labor Force Participation PatentsRD : Patents, R\&D and Technological Spillovers for a Panel of Firms Train : Stated Preferences for Train Traveling Unemployment : Unemployment Duration University : Provision of University Teaching and Research Workinghours : Wife Working Hours Journal of Business Economics and Statistics web site : http://amstat.tandfonline.com/loi/ubes20 Benefits : Unemployment of Blue Collar Workers Catsup : Choice of Brand for Catsup Cracker : Choice of Brand for Crakers Kakadu : Willingness to Pay for the Preservation of the Kakadu National Park Ketchup : Choice of Brand for Ketchup LaborSupply : Wages and Hours Worked Mofa : International Expansion of U.S. Mofa's (majority--owned Foreign Affiliates in Fire (finance, Insurance and Real Estate) Somerville : Visits to Lake Somerville Tuna : Choice of Brand for Tuna Yogurt : Choice of Brand for Yogurts Journal of Statistics Education's data archive : http://www.amstat.org/publications/jse/jse_data_archive.htm Diamond : Pricing the C's of Diamond Stones FriendFoe : Data from the Television Game Show Friend Or Foe ? Kenneth Train's home page : http://elsa.berkeley.edu/~train/ HC : Heating and Cooling System Choice in Newly Built Houses in California Heating : Heating System Choice in California Houses Mode : Mode Choice Baltagi, Badi H. (2003) Econometric analysis of panel data, John Wiley and sons, http://www.wiley.com/legacy/wileychi/baltagi/ Cigar : Cigarette Consumption Crime : Crime in North Carolina Gasoline : Gasoline Consumption Grunfeld : Grunfeld Investment Data Hedonic : Hedonic Prices of Census Tracts in Boston Produc : Us States Production Wages : Panel Datas of Individual Wages Cameron, A.C. and P.K. Trivedi (2005) Microeconometrics : methods and applications, Cambridge DoctorContacts : Contacts With Medical Doctor Fishing : Choice of Fishing Mode LaborSupply : Wages and Hours Worked MedExp : Structure of Demand for Medical Care PSID : Panel Survey of Income Dynamics PatentsHGH : Dynamic Relation Between Patents and R\&D RetSchool : Return to Schooling StrikeDur : Strikes Duration Treatment : Evaluating Treatment Effect of Training on Earnings UnempDur : Unemployment Duration VietNamH : Medical Expenses in Viet--nam (household Level) VietNamI : Medical Expenses in Viet--nam (individual Level) Cameron, A.C. and Trivedi P.K. (1998) Regression analysis of count data, Cambridge University Press, http://cameron.econ.ucdavis.edu/racd/racddata.html Bids : Bids Received By U.S. Firms DoctorAUS : Doctor Visits in Australia OFP : Visits to Physician Office PatentsHGH : Dynamic Relation Between Patents and R\&D Somerville : Visits to Lake Somerville StrikeNb : Number of Strikes in Us Manufacturing Davidson, R. and James G. MacKinnon (2004) Econometric Theory and Methods, New York, Oxford University Press, http://www.econ.queensu.ca/ETM/ CRSPday : Daily Returns from the CRSP Database CRSPmon : Monthly Returns from the CRSP Database Consumption : Quarterly Data on Consumption and Expenditure Doctor : Number of Doctor Visits Earnings : Earnings for Three Age Groups Hstarts : Housing Starts MW : Growth of Disposable Income and Treasury Bill Rate Money : Money, GDP and Interest Rate in Canada Participation : Labor Force Participation Tbrate : Interest Rate, GDP and Inflation Greene, W.H. (2003) Econometric Analysis, Prentice Hall, http://www.prenhall.com/greene/greene1.html Accident : Ship Accidents Airline : Cost for U.S. Airlines Electricity : Cost Function for Electricity Producers Fair : Extramarital Affairs Data Grunfeld : Grunfeld Investment Data Klein : Klein's Model I Longley : The Longley Data ManufCost : Manufacturing Costs Metal : Production for SIC 33 ModeChoice : Data to Study Travel Mode Choice Mroz : Labor Supply Data MunExp : Municipal Expenditure Data Nerlove : Cost Function for Electricity Producers, 1955 Solow : Solow's Technological Change Data Strike : Strike Duration Data TranspEq : Statewide Data on Transportation Equipment Manufacturing Hayashi, F. (2000) Econometrics, Princeton University Press, http://fhayashi.fc2web.com/hayashi_econometrics.htm DM : DM Dollar Exchange Rate Electricity : Cost Function for Electricity Producers Griliches : Wage Datas LT : Dollar Sterling Exchange Rate Mishkin : Inflation and Interest Rates Mpyr : Money, National Product and Interest Rate Nerlove : Cost Function for Electricity Producers, 1955 Pound : Pound-dollar Exchange Rate SumHes : The Penn Table Yen : Yen-dollar Exchange Rate Stock, James H. and Mark W. Watson (2003) Introduction to Econometrics, Addison-Wesley Educational Publishers CPSch3 : Earnings from the Current Population Survey Caschool : The California Test Score Data Set Cigarette : The Cigarette Consumption Panel Data Set Fatality : Drunk Driving Laws and Traffic Deaths Hmda : The Boston HMDA Data Set Journals : Economic Journals Dat Set MCAS : The Massachusetts Test Score Data Set Macrodat : Macroeconomic Time Series for the United States Orange : The Orange Juice Data Set Star : Effects on Learning of Small Class Sizes Verbeek, Marno (2004) A Guide to Modern Econometrics, John Wiley and Sons Airq : Air Quality for Californian Metropolitan Areas Benefits : Unemployment of Blue Collar Workers Bwages : Wages in Belgium Capm : Stock Market Data Clothing : Sales Data of Men's Fashion Stores Forward : Exchange Rates of US Dollar Against Other Currencies Garch : Daily Observations on Exchange Rates of the US Dollar Against Other Currencies Housing : Sales Prices of Houses in the City of Windsor Icecream : Ice Cream Consumption IncomeUK : Seasonally Unadjusted Quarterly Data on Disposable Income and Expenditure Irates : Monthly Interest Rates Labour : Belgian Firms Males : Wages and Education of Young Males MoneyUS : Macroeconomic Series for the United States NaturalPark : Willingness to Pay for the Preservation of the Alentejo Natural Park PE : Price and Earnings Index PPP : Exchange Rates and Price Indices for France and Italy PatentsRD : Patents, R\&D and Technological Spillovers for a Panel of Firms Pricing : Returns of Size-based Portfolios SP500 : Returns on Standard \& Poor's 500 Index Schooling : Wages and Schooling Tobacco : Households Tobacco Budget Share Wages1 : Wages, Experience and Schooling
Function Index.Observations [Ecdat v0.3-1]
keywords
documentation
title
Observations
description
country Consumption : Quarterly Data on Consumption and Expenditure DM : DM Dollar Exchange Rate Garch : Daily Observations on Exchange Rates of the US Dollar Against Other Currencies Gasoline : Gasoline Consumption Hstarts : Housing Starts Icecream : Ice Cream Consumption IncomeUK : Seasonally Unadjusted Quarterly Data on Disposable Income and Expenditure Irates : Monthly Interest Rates Klein : Klein's Model I LT : Dollar Sterling Exchange Rate Longley : The Longley Data MW : Growth of Disposable Income and Treasury Bill Rate Macrodat : Macroeconomic Time Series for the United States ManufCost : Manufacturing Costs Mishkin : Inflation and Interest Rates Mofa : International Expansion of U.S. Mofa's (majority--owned Foreign Affiliates in Fire (finance, Insurance and Real Estate) Money : Money, GDP and Interest Rate in Canada Mpyr : Money, National Product and Interest Rate Orange : The Orange Juice Data Set PE : Price and Earnings Index PPP : Exchange Rates and Price Indices for France and Italy Pound : Pound-dollar Exchange Rate Solow : Solow's Technological Change Data StrikeNb : Number of Strikes in Us Manufacturing SumHes : The Penn Table Tbrate : Interest Rate, GDP and Inflation Yen : Yen-dollar Exchange Rate goods Computers : Prices of Personal Computers Diamond : Pricing the C's of Diamond Stones Housing : Sales Prices of Houses in the City of Windsor Journals : Economic Journals Dat Set households BudgetFood : Budget Share of Food for Spanish Households BudgetItaly : Budget Shares for Italian Households BudgetUK : Budget Shares of British Households HC : Heating and Cooling System Choice in Newly Built Houses in California Heating : Heating System Choice in California Houses VietNamH : Medical Expenses in Viet--nam (household Level) individuals Benefits : Unemployment of Blue Collar Workers Bwages : Wages in Belgium CPSch3 : Earnings from the Current Population Survey Car : Stated Preferences for Car Choice Catsup : Choice of Brand for Catsup Cracker : Choice of Brand for Crakers Doctor : Number of Doctor Visits DoctorAUS : Doctor Visits in Australia Earnings : Earnings for Three Age Groups Fair : Extramarital Affairs Data Fishing : Choice of Fishing Mode FriendFoe : Data from the Television Game Show Friend Or Foe ? Griliches : Wage Datas HI : Health Insurance and Hours Worked By Wives Hmda : The Boston HMDA Data Set Kakadu : Willingness to Pay for the Preservation of the Kakadu National Park Ketchup : Choice of Brand for Ketchup Males : Wages and Education of Young Males Mathlevel : Level of Calculus Attained for Students Taking Advanced Micro--economics Mode : Mode Choice ModeChoice : Data to Study Travel Mode Choice Mroz : Labor Supply Data NaturalPark : Willingness to Pay for the Preservation of the Alentejo Natural Park OFP : Visits to Physician Office PSID : Panel Survey of Income Dynamics Participation : Labor Force Participation RetSchool : Return to Schooling Schooling : Wages and Schooling Somerville : Visits to Lake Somerville Star : Effects on Learning of Small Class Sizes Tobacco : Households Tobacco Budget Share Train : Stated Preferences for Train Traveling Tuna : Choice of Brand for Tuna Unemployment : Unemployment Duration VietNamI : Medical Expenses in Viet--nam (individual Level) Wages : Panel Datas of Individual Wages Wages1 : Wages, Experience and Schooling Workinghours : Wife Working Hours Yogurt : Choice of Brand for Yogurts production units Airline : Cost for U.S. Airlines Bids : Bids Received By U.S. Firms CRSPday : Daily Returns from the CRSP Database CRSPmon : Monthly Returns from the CRSP Database Clothing : Sales Data of Men's Fashion Stores Electricity : Cost Function for Electricity Producers Grunfeld : Grunfeld Investment Data Labour : Belgian Firms Nerlove : Cost Function for Electricity Producers, 1955 Oil : Oil Investment PatentsHGH : Dynamic Relation Between Patents and R\&D PatentsRD : Patents, R\&D and Technological Spillovers for a Panel of Firms regional Airq : Air Quality for Californian Metropolitan Areas Cigar : Cigarette Consumption Cigarette : The Cigarette Consumption Panel Data Set Crime : Crime in North Carolina Fatality : Drunk Driving Laws and Traffic Deaths Hedonic : Hedonic Prices of Census Tracts in Boston Metal : Production for SIC 33 MunExp : Municipal Expenditure Data Produc : Us States Production TranspEq : Statewide Data on Transportation Equipment Manufacturing schools Caschool : The California Test Score Data Set MCAS : The Massachusetts Test Score Data Set University : Provision of University Teaching and Research
Function 03.ReadingData [limma v3.28.14]
keywords
documentation
title
Topic: Reading Microarray Data from Files
description
This help page gives an overview of LIMMA functions used to read data from files.
Function 04.Background [limma v3.28.14]
keywords
documentation
title
Topic: Background Correction
description
This page deals with background correction methods provided by the backgroundCorrect, kooperberg or neqc functions. Microarray data is typically background corrected by one of these functions before normalization and other downstream analysis. backgroundCorrect works on matrices, EListRaw or RGList objects, and calls backgroundCorrect.matrix. The movingmin method of backgroundCorrect uses utility functions ma3x3.matrix and ma3x3.spottedarray. The normexp method of backgroundCorrect uses utility functions normexp.fit and normexp.signal. kooperberg is a Bayesian background correction tool designed specifically for two-color GenePix data. It is computationally intensive and requires several additional columns from the GenePix data files. These can be read in using read.maimages and specifying the other.columns argument. neqc is for single-color data. It performs normexp background correction and quantile normalization using control probes. It uses utility functions normexp.fit.control and normexp.signal. If robust=TRUE, then normexp.fit.control uses the function huber in the MASS package.
Function limmaUsersGuide [limma v3.28.14]
keywords
documentation
title
View Limma User's Guide
description
Finds the location of the Limma User's Guide and optionally opens it.
Function 11.RNAseq [limma v3.28.14]
keywords
documentation
title
Topic: Analysis of RNA-seq Data
description
This page gives an overview of LIMMA functions to analyze RNA-seq data. voom Transform RNA-seq or ChIP-seq counts to log counts per million (log-cpm) with associated precision weights. After this tranformation, RNA-seq or ChIP-seq data can be analyzed using the same functions as would be used for microarray data. voomWithQualityWeights Combines the functionality of voom and arrayWeights. diffSplice Test for differential exon usage between experimental conditions. topSplice Show a data.frame of top results from diffSplice. plotSplice Plot results from diffSplice. plotExons Plot logFC for individual exons for a given gene.
Function 09.Diagnostics [limma v3.28.14]
keywords
documentation
title
Topic: Diagnostics and Quality Assessment
description
This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots. This package provides an anova method which is designed for assessing the quality of an array series or of a normalization method. It is not designed to assess differential expression of individual genes. anova uses utility functions bwss and bwss.matrix. The function arrayWeights estimates the empirical reliability of each array following a linear model fit. Diagnostic plots can be produced by imageplot Produces a spatial picture of any spot-specific measure from an array image. If the log-ratios are plotted, then this produces an in-silico representation of the well known false-color TIFF image of an array. imageplot3by2 will write imageplots to files, six plots to a page. plotFB Plots foreground versus background log-intensies. plotMD Mean-difference plots. Very versatile plot. For two color arrays, this plots the M-values vs A-values. For single channel technologies, this plots one column of log-expression values vs the average of the other columns. For fitted model objects, this plots a log-fold-change versus average log-expression. mdplot can also be useful for comparing two one-channel microarrays. plotMA MA-plots, essentially the same as mean-difference plots. plotMA3by2 will write MA-plots to files, six plots to a page. plotWithHighlights Scatterplots with highlights. This is the underlying engine for plotMD and plotMA. plotPrintTipLoess Produces a grid of MA-plots, one for each print-tip group on an array, together with the corresponding lowess curve. Intended to help visualize print-tip loess normalization. plotPrintorder For an array, produces a scatter plot of log-ratios or log-intensities by print order. plotDensities Individual channel densities for one or more arrays. An essential plot to accompany between array normalization, especially quantile normalization. plotMDS Multidimensional scaling plot for a set of arrays. Useful for visualizing the relationship between the set of samples. plotSA Sigma vs A plot. After a linear model is fitted, this checks constancy of the variance with respect to intensity level. plotPrintTipLoess uses utility functions gridr and gridc. plotDensities uses utility function RG.MA.