A B C D E F G H I K L M N P Q R S T U V W Z misc
01.Introduction | Introduction to the LIMMA Package |
02.Classes | Classes Defined by this Package |
03.ReadingData | Reading Microarray Data from Files |
04.Background | Background Correction |
05.Normalization | Normalization of Microarray Data |
06.LinearModels | Linear Models for Microarrays |
07.SingleChannel | Individual Channel Analysis of Two-Color Microarrays |
08.Tests | Hypothesis Testing for Linear Models |
09.Diagnostics | Diagnostics and Quality Assessment |
10.Other | Other Functions |
alias2Symbol | Convert Gene Alias to Official Gene Symbols |
anova.MAList | ANOVA Table - method |
array2channel | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel |
arrayWeights | Array Quality Weights |
arrayWeightsQuick | Array Quality Weights |
arrayWeightsSimple | Array Quality Weights |
as.data.frame.MArrayLM | Turn a Microarray Linear Model Object into a Dataframe |
as.MAList | Convert marrayNorm Object to an MAList Object |
as.matrix.EList | Turn a Microarray Data Object into a Matrix |
as.matrix.EListRaw | Turn a Microarray Data Object into a Matrix |
as.matrix.ExpressionSet | Turn a Microarray Data Object into a Matrix |
as.matrix.LumiBatch | Turn a Microarray Data Object into a Matrix |
as.matrix.MAList | Turn a Microarray Data Object into a Matrix |
as.matrix.MArrayLM | Turn a Microarray Data Object into a Matrix |
as.matrix.marrayNorm | Turn a Microarray Data Object into a Matrix |
as.matrix.PLMset | Turn a Microarray Data Object into a Matrix |
as.matrix.RGList | Turn a Microarray Data Object into a Matrix |
as.matrix.vsn | Turn a Microarray Data Object into a Matrix |
asMatrixWeights | asMatrixWeights |
auROC | Area Under Receiver Operating Curve |
avedups | Average Over Duplicate Spots |
avedups.default | Average Over Duplicate Spots |
avedups.MAList | Average Over Duplicate Spots |
avereps | Average Over Irregular Replicate Spots |
avereps.default | Average Over Irregular Replicate Spots |
avereps.MAList | Average Over Irregular Replicate Spots |
backgroundCorrect | Correct Intensities for Background |
barcodeplot | Gene Set Test |
blockDiag | Block Diagonal Matrix |
bwss | Between and within sums of squares |
bwss.matrix | Between and within sums of squares for matrix |
cbind.EList | Combine RGList, MAList, EList or EListRaw Objects |
cbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects |
cbind.MAList | Combine RGList, MAList, EList or EListRaw Objects |
cbind.RGList | Combine RGList, MAList, EList or EListRaw Objects |
changeLog | Limma Change Log |
classifyTestsF | Multiple Testing Genewise Across Contrasts |
classifyTestsP | Multiple Testing Genewise Across Contrasts |
classifyTestsT | Multiple Testing Genewise Across Contrasts |
coerce,RGList,exprSet2-method | Red, Green Intensity List - class |
contrasts.fit | Compute Contrasts from Linear Model Fit |
controlStatus | Set Status of each Spot from List of Spot Types |
convest | Estimate Proportion of True Null Hypotheses |
decideTests | Multiple Testing Across Genes and Contrasts |
designI2A | Convert Individual Channel Design Matrix to M-A Format |
designI2M | Convert Individual Channel Design Matrix to M-A Format |
dim.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
dim.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
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.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames<-.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames<-.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames<-.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
dimnames<-.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
duplicateCorrelation | Correlation Between Duplicates |
eBayes | Empirical Bayes Statistics for Differential Expression |
ebayes | Empirical Bayes Statistics for Differential Expression |
EList-class | Expression List - class |
EListRaw-class | Expression List - class |
exprs.MA | Extract Log-Expression Matrix from MAList |
fitFDist | Moment Estimation of Scaled F-Distribution |
fitted.MArrayLM | Fitted Values Method for MArrayLM Fits |
FStat | Multiple Testing Genewise Across Contrasts |
geneSetTest | Gene Set Test |
getDupSpacing | Extract the Print Layout of an Array from the GAL File |
getEAWP | Extract Basic Data from Microarray Data Objects |
getLayout | Extract the Print Layout of an Array from the GAL File |
getLayout2 | Extract the Print Layout of an Array from the GAL File |
getSpacing | Get Numerical Spacing |
gls.series | Fit Linear Model to Microarray Data by Generalized Least Squares |
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 |
imageplot3by2 | Write Imageplots to Files |
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.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
length.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
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 |
limma | Introduction to the LIMMA Package |
limmaUsersGuide | View Limma User's Guide |
lm.series | Fit Linear Model to Microrray Data by Ordinary Least Squares |
lmFit | Linear Model for Series of Arrays |
lmscFit | Fit Linear Model to Individual Channels of Two-Color Data |
loessFit | Fast Simple Loess |
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 |
mdplot | mdplot |
merge.MAList | Merge RGList or MAList Data Objects |
merge.RGList | Merge RGList or MAList Data Objects |
mergeScans | Merge two scans of two-color arrays |
mergeScansRG | Merge two scans of two-color arrays |
modelMatrix | Construct Design Matrix |
modifyWeights | modifyWeights |
mrlm | Fit Linear Model to Microrray Data by Robust Regression |
nonEstimable | Check for Full Column Rank |
normalizeBetweenArrays | Normalize Between Arrays |
normalizeForPrintorder | Print-Order Normalization |
normalizeForPrintorder.rg | Print-Order Normalization |
normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute Value |
normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles |
normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
normalizeWithinArrays | Normalize Within Arrays |
normexp.fit | Fit Normal+Exp Convolution Model to Observed Intensities |
normexp.signal | Expected Signal Given Observed Foreground Under Normal+Exp Model |
plotDensities | Individual-channel Densities Plot |
plotFB | FB-Plot |
plotlines | plotlines |
plotMA | MA-Plot |
plotMA3by2 | Write MA-Plots to Files |
plotMDS | Multidimensional scaling plot of microarray data |
plotPrintorder | Print-Order Normalization |
plotPrintTipLoess | MA Plots by Print-Tip Group |
plotSA | Sigma vs A plot for microarray linear model |
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 |
printtipWeights | Sub-array Quality Weights |
printtipWeightsSimple | Sub-array Quality Weights |
protectMetachar | Protect Metacharacters |
qqt | Student's t Quantile-Quantile Plot |
QualityWeights | Spot Quality Weights |
rbind.EList | Combine RGList, MAList, EList or EListRaw Objects |
rbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects |
rbind.MAList | Combine RGList, MAList, EList or EListRaw Objects |
rbind.RGList | Combine RGList, MAList, EList or EListRaw Objects |
read.columns | Read specified columns from a file |
read.imagene | Read RGList or EListRaw from Image Analysis Output Files |
read.maimages | Read RGList or EListRaw from Image Analysis Output Files |
readGAL | Read a GAL file |
readGenericHeader | Read Header Information from Image Analysis Raw Data File |
readGPRHeader | Read Header Information from Image Analysis Raw Data File |
readImaGeneHeader | Read ImaGene Header Information |
readSMDHeader | Read Header Information from Image Analysis Raw Data File |
readSpotTypes | Read Spot Types File |
readTargets | Read Targets File |
removeBatchEffect | Remove Batch Effect |
removeExt | Remove Common Extension from File Names |
residuals.MArrayLM | Extract Residuals from MArrayLM Fit |
RG.MA | Normalize Within Arrays |
RGList-class | Red, Green Intensity List - class |
roast | Rotation Gene Set Tests |
romer | Rotation Gene Set Enrichment Analysis |
selectModel | Select Appropriate Linear Model |
show,LargeDataObject-method | Large Data Object - class |
show,TestResults-method | Matrix of Test Results - class |
spotc | Row and Column Positions on Microarray |
spotr | Row and Column Positions on Microarray |
squeezeVar | Smooth Sample Variances |
strsplit2 | Split Composite Names |
summary.EList | Summaries of Microarray Data Objects |
summary.EListRaw | Summaries of Microarray Data Objects |
summary.MAList | Summaries of Microarray Data Objects |
summary.MArrayLM | Summaries of Microarray Data Objects |
summary.RGList | Summaries of Microarray Data Objects |
summary.TestResults | Matrix of Test Results - class |
symbols2indices | Make Gene Set Indices from Symbols |
targetsA2C | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel |
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 |
topTableF | Table of Top Genes from Linear Model Fit |
topTreat | Table of Top Genes from Linear Model Fit |
treat | Empirical Bayes Statistics for Differential Expression |
trigammaInverse | Inverse Trigamma Function |
trimWhiteSpace | Trim Leading and Trailing White Space |
tZscore | Z-score Equivalents |
uniquegenelist | Eliminate Duplicate Names from the Gene List |
uniqueTargets | Construct Design Matrix |
unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns |
vennCounts | Venn Diagrams |
vennDiagram | Venn Diagrams |
volcanoplot | Volcano Plot |
weighted.median | Weighted Median |
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 |
[.EList | Subset RGList, MAList, EList or MArrayLM Objects |
[.EListRaw | Subset RGList, MAList, EList or MArrayLM Objects |
[.MAList | Subset RGList, MAList, EList or MArrayLM Objects |
[.MArrayLM | Subset RGList, MAList, EList or MArrayLM Objects |
[.RGList | Subset RGList, MAList, EList or MArrayLM Objects |