A B C D E F G H I K L M N P Q R S T U V W Z misc
1.Introduction | Introduction to the LIMMA Package |
2.Classes | Classes Defined by this Package |
3.ReadingData | Reading Microarray Data from Files |
4.Normalization | Normalization of Microarray Data |
5.LinearModels | Linear Models for Microarrays |
6.SingleChannel | Single Channel Analysis of Two-Color Microarrays |
7.Diagnostics | Diagnostics and Quality Assessment |
8.Other | Other Functions |
a.spot | Extract M or A-values from SPOT data.frame or matrix |
anova.MAList | ANOVA Table - method |
array2channel | Convert Two-Color Targets File to One-Row-Per-Channel |
as.MAList | Convert marrayNorm Object to an MAList Object |
auROC | Area Under Receiver Operating Curve |
backgroundCorrect | Correct Intensities for Background |
blockDiag | Block Diagonal Matrix |
bwss | Between and within sums of squares |
bwss.matrix | Between and within sums of squares for matrix |
cbind.MAList | Combine RGList or MAList Objects |
cbind.RGList | Combine RGList or MAList Objects |
classifyTests | Treat Simultaneous T-Tests as Classification Problem |
classifyTestsF | Treat Simultaneous T-Tests as Classification Problem |
classifyTestsP | Treat Simultaneous T-Tests as Classification Problem |
classifyTestsT | Treat Simultaneous T-Tests as Classification Problem |
coerce,RGList,exprSet2-method | Red, Green Intensity List - class |
contrasts.fit | Contrast Information from Linear Model Fit |
controlStatus | Set Status of each Spot from List of Spot Types |
designMatrix | Construct Design Matrix |
dim.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
dim.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
dim.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
dimnames.MAList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
dupcor.series | Correlation Between Duplicates |
duplicateCorrelation | Correlation Between Duplicates |
eBayes | Empirical Bayes Statistics for Differential Expression |
ebayes | Empirical Bayes Statistics for Differential Expression |
exprSet2-class | Expression Set - class |
fitFDist | Moment Estimation of Scaled F-Distribution |
FStat | Treat Simultaneous T-Tests as Classification Problem |
getLayout | Extract the Print Layout of an Array from the GAL File |
getSpacing | Get Numerical Spacing |
gls.series | Generalized Least Squares for Series of Microarrays |
gridc | Row and Column Positions on Microarray |
gridr | Row and Column Positions on Microarray |
heatDiagram | Stemmed Heat Diagram |
heatdiagram | Stemmed Heat Diagram |
helpMethods | Prompt for Method Help Topics |
imageplot | Image Plot of Microarray Statistics |
intraspotCorrelation | Intra-Spot Correlation for Two Color Data |
is.fullrank | Check for Full Column Rank |
isNumeric | Test for Numeric Argument |
kooperberg | Kooperberg Model-Based Background Correction |
LargeDataObject-class | Large Data Object - class |
length.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
length.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
length.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
limmaguideURL | File Location of html Limma User's Guide |
lm.series | Linear Model for Series of Arrays |
lmFit | Linear Model for Series of Arrays |
lmscFit | Single Channel Linear Model for Series of Arrays |
loessFit | Fast Simple Loess |
m.spot | Extract M or A-values from SPOT data.frame or matrix |
MA.RG | Normalize Within Arrays |
ma3x3.matrix | Two dimensional Moving Averages with 3x3 Window |
ma3x3.spottedarray | Two dimensional Moving Averages with 3x3 Window |
makeContrasts | Construct Matrix of Custom Contrasts |
makeUnique | Make Values of Character Vector Unique |
MAList-class | M-value, A-value Expression List - class |
MArrayLM-class | Microarray Linear Model Fit - class |
matvec | Multiply a Matrix by a Vector |
merge.MAList | Merge RGList or MAList Data Objects |
merge.RGList | Merge RGList or MAList Data Objects |
modelMatrix | Construct Design Matrix |
modifyWeights | modifyWeights |
normalizeBetweenArrays | Normalize Between Arrays |
normalizeForPrintorder | Print-Order Normalization |
normalizeMedianDeviations | Normalize Columns of a Matrix to have the Same Scale |
normalizeMedians | Normalize Columns of a Matrix to have the Same Scale |
normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles |
normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
normalizeWithinArrays | Normalize Within Arrays |
plotDensities | Single-channel Densities Plot |
plotMA | MA-Plot |
plotPrintorder | Print-Order Normalization |
plotPrintTipLoess | MA Plots by Print-Tip Group |
poolVar | Pool Sample Variances with Unequal Variances |
printHead | Print Leading Rows of Large Objects |
PrintLayout-class | Print Layout - class |
printorder | Identify Order in which Spots were Printed |
qqt | Student's t Quantile-Quantile Plot |
QualityWeights | Spot Quality Weights |
rbind.MAList | Combine RGList or MAList Objects |
rbind.RGList | Combine RGList or MAList Objects |
read.imagene | Read RGList from Image Analysis Output Files |
read.maimages | Read RGList from Image Analysis Output Files |
read.matrix | Read Matrix with Headers from File |
read.series | Read series of image files |
readGAL | Read a GAL file |
readGPRHeaders | Read GenePix Results File Header Information |
readImageneHeaders | Read Imagene Header Information |
readSpotTypes | Read Spot Types File |
readTargets | Read RNA Targets File |
removeExt | Remove Common Extension from File Names |
rg.genepix | Extract RGList from data.frames Containing Genepix Data |
RG.MA | Normalize Within Arrays |
rg.quantarray | Extract RGList from data.frames Containing Quantarray Data |
rg.series.spot | Read RGList from SPOT Image Analysis Output Files |
rg.spot | Extract RGList from data.frames Containing SPOT Data |
RGList-class | Red, Green Intensity List - class |
rlm.series | Robust Linear Model for Series of Microarrays |
show,LargeDataObject-method | Large Data Object - class |
show,TestResults-method | Matrix of Test Results - class |
splitName | Split Composite Gene Names |
spotc | Row and Column Positions on Microarray |
spotr | Row and Column Positions on Microarray |
squeezeVar | Smooth Sample Variances |
summary.TestResults | Matrix of Test Results - class |
TestResults-class | Matrix of Test Results - class |
tmixture.matrix | Estimate Scale Factor in Mixture of t-Distributions |
tmixture.vector | Estimate Scale Factor in Mixture of t-Distributions |
topTable | Table of Top Genes from Linear Model Fit |
toptable | Table of Top Genes from Linear Model Fit |
trigammaInverse | Inverse Trigamma Function |
uniquegenelist | Eliminate Duplicate Names from the Gene List |
uniqueTargets | Construct Design Matrix |
unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns |
vecmat | Multiply a Matrix by a Vector |
vennCounts | Venn Diagrams |
vennDiagram | Venn Diagrams |
write.fit | Write MArrayLM Object to a File |
wtarea | Spot Quality Weights |
wtflags | Spot Quality Weights |
wtIgnore.Filter | Spot Quality Weights |
zscoreGamma | z-score equivalents |
zscoreT | z-score equivalents |
[.MAList | Subset RGList or MAList Objects |
[.RGList | Subset RGList or MAList Objects |