01Introduction | Introduction to the LIMMA Package |
02classes | Topic: Classes Defined by this Package |
03reading | Topic: Reading Microarray Data from Files |
04Background | Topic: Background Correction |
05Normalization | Topic: Normalization of Microarray Data |
06linearmodels | Topic: Linear Models for Microarrays |
07SingleChannel | Topic: Individual Channel Analysis of Two-Color Microarrays |
08Tests | Topic: Hypothesis Testing for Linear Models |
09Diagnostics | Topic: Diagnostics and Quality Assessment |
10GeneSetTests | Topic: Gene Set Tests |
11RNAseq | Topic: Analysis of RNA-seq Data |
alias2Symbol | Convert Gene Aliases to Official Gene Symbols |
anova-method | ANOVA Table - method |
arrayWeights | Array Quality Weights |
arrayWeightsQuick | Array Quality Weights |
asdataframe | Turn a Microarray Linear Model Object into a Dataframe |
asmalist | Convert marrayNorm Object to an MAList Object |
asmatrix | Turn a Microarray Data Object into a Matrix |
asMatrixWeights | asMatrixWeights |
auROC | Area Under Receiver Operating Curve |
avearrays | Average Over Replicate Arrays |
avedups | Average Over Duplicate Spots |
avereps | Average Over Irregular Replicate Probes |
backgroundcorrect | Correct Intensities for Background |
barcodeplot | Barcode Enrichment Plot |
beadCountWeights | Bead Count Weights for Illumina BeadChips |
blockDiag | Block Diagonal Matrix |
bwss | Between and within sums of squares |
bwss.matrix | Between and within sums of squares for matrix |
camera | Competitive Gene Set Test Accounting for Inter-gene... |
cbind | Combine RGList, MAList, EList or EListRaw Objects |
changelog | Change Log |
channel2M | Convert Individual Channel Design Matrix to M-A Format |
chooseLowessSpan | Choose Span for Local-Weighted Regression Smoothing |
classifytestsF | Genewise Nested F-Tests |
contrastAsCoef | Reform a Design Matrix to that Contrasts Become Coefficients |
contrasts.fit | Compute Contrasts from Linear Model Fit |
controlStatus | Set Status of each Spot from List of Spot Types |
coolmap | Heatmap of gene expression values |
cumOverlap | Cumulative Overlap Analysis of Ordered Lists |
decideTests | Multiple Testing Across Genes and Contrasts |
detectionPValue | Detection P-Values from Negative Controls |
diffSplice | Test for Differential Splicing |
dim | Retrieve the Dimensions of an RGList, MAList or MArrayLM... |
dimnames | Retrieve the Dimension Names of an RGList, MAList, EList,... |
dupcor | Correlation Between Duplicates or Within Blocks |
ebayes | Empirical Bayes Statistics for Differential Expression |
EList | Expression List (EList) class |
exprsMA | Extract Log-Expression Matrix from MAList |
fitfdist | Moment Estimation of Scaled F-Distribution |
fitGammaIntercept | Fit Intercept to Vector of Gamma Distributed Variates |
fitmixture | Fit Mixture Model by Non-Linear Least Squares |
fitted.MArrayLM | Fitted Values Method for MArrayLM Fits |
genas | Genuine Association of Gene Expression Profiles |
geneSetTest | Mean-rank Gene Set Test |
getEAWP | Extract Basic Data from Expression Data Objects |
getlayout | 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... |
goana | Gene Ontology or KEGG Pathway Analysis |
gridspotrc | Row and Column Positions on Microarray |
head | Return the First to Last Part of a Data Object |
heatdiagram | Stemmed Heat Diagram |
helpMethods | Prompt for Method Help Topics |
ids2indices | Convert Gene Identifiers to Indices for Gene Sets |
imageplot | Image Plot of Microarray Statistics |
imageplot3by2 | Write Imageplots to Files |
intraspotCorrelation | Intra-Spot Correlation for Two Color Data |
isfullrank | Check for Full Column Rank |
isnumeric | Test for Numeric Argument |
kooperberg | Kooperberg Model-Based Background Correction for GenePix data |
LargeDataObject | Large Data Object - class |
limmaUsersGuide | View Limma User's Guide |
lmFit | Linear Model for Series of Arrays |
lmscFit | Fit Linear Model to Individual Channels of Two-Color Data |
lm.series | Fit Linear Model to Microrray Data by Ordinary Least Squares |
loessfit | Univariate Lowess With Prior Weights |
logcosh | Logarithm of cosh |
logsumexp | Log Sum of Exponentials |
ma3x3 | Two dimensional Moving Averages with 3x3 Window |
makeContrasts | Construct Matrix of Custom Contrasts |
makeunique | Make Values of Character Vector Unique |
malist | M-value, A-value Expression List - class |
marraylm | Microarray Linear Model Fit - class |
mdplot | Mean-Difference Plot |
merge | Merge RGList or MAList Data Objects |
mergeScansRG | Merge two scans of two-color arrays |
modelMatrix | Construct Design Matrix |
modifyWeights | Modify Matrix of Weights By Control Status of Rows |
mrlm | Fit Linear Model to Microrray Data by Robust Regression |
nec | NormExp Background Correction and Normalization Using Control... |
normalizebetweenarrays | Normalize Between Arrays |
normalizeCyclicLoess | Normalize Columns of a Matrix by Cyclic Loess |
normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute... |
normalizeprintorder | Print-Order Normalization |
normalizequantiles | Normalize Columns of a Matrix to have the same Quantiles |
normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
normalizeVSN | Variance Stabilizing Normalization (vsn) |
normalizeWithinArrays | Normalize Within Arrays |
normexpfit | Fit Normal+Exp Convolution Model to Observed Intensities |
normexpfitcontrol | Normexp Model Parameter Estimation Aided by Negative Controls |
normexpfitdetectionp | Estimate Normexp Model Parameter Using Negative Controls... |
normexpsignal | Expected Signal Given Observed Foreground Under Normal+Exp... |
plotDensities | Plot Expression Densities |
plotExonJunc | Differential splicing plot with junctions |
plotExons | Plot exons of differentially expressed gene |
plotFB | FB-Plot |
plotlines | plotlines |
plotma | MA-Plot of Expression Data |
plotma3by2 | Write MA-Plots to Files |
plotMD | Mean-Difference Plot of Expression Data |
plotMDS | Multidimensional scaling plot of distances between gene... |
plotprinttiploess | MA Plots by Print-Tip Group |
plotRLDF | Plot of regularized linear discriminant functions for... |
plotSA | Sigma vs A plot for microarray linear model |
plotSplice | Differential splicing plot |
plotWithHighlights | Scatterplot With Highlighting of Special Points |
poolvar | Pool Sample Variances with Unequal Variances |
predFCm | Predictive log fold change for microarrays |
printHead | Print Leading Rows of Large Objects |
PrintLayout | Print Layout - class |
printorder | Identify Order in which Spots were Printed |
printtipWeights | Sub-array Quality Weights |
propexpr | Estimate Proportion of Expressed Probes |
propTrueNull | Estimate Proportion of True Null Hypotheses |
protectMetachar | Protect Metacharacters |
qqt | Student's t or Fisher's F Quantile-Quantile Plot |
qualwt | Spot Quality Weights for Spotted Microarrays |
rankSumTestwithCorrelation | Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For... |
read.columns | Read specified columns from a file |
readgal | Read a GAL file |
readGPRHeader | Read Header Information from Microarray Raw Data File |
read.idat | Read Illumina expression data from IDAT files |
read.ilmn | Read Illumina Expression Data |
read.ilmn.targets | Read Illumina Data from a Target Dataframe |
readImaGeneHeader | Read ImaGene Header Information |
read.maimages | Read RGList or EListRaw from Image Analysis Output Files |
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 |
rglist | Red, Green Intensity List - class |
roast | Rotation Gene Set Tests |
romer | Rotation Gene Set Enrichment Analysis |
selectmodel | Select Appropriate Linear Model |
squeezeVar | Squeeze Sample Variances |
strsplit2 | Split Composite Names |
subsetting | Subset RGList, MAList, EListRaw, EList, MArrayLM or... |
summary | Summaries of Microarray Data Objects |
targetsA2C | Convert Two-Color Targets Dataframe from One-Row-Per-Array to... |
TestResults | Matrix of Test Results - class |
tmixture | Estimate Scale Factor in Mixture of t-Distributions |
topGO | Table of Top GO Terms or Top KEGG Pathways |
topRomer | Top Gene Set Testing Results from Romer |
topSplice | Top table of differentially spliced genes or exons |
toptable | Table of Top Genes from Linear Model Fit |
tricubeMovingAverage | Moving Average Smoother With Tricube Weights |
trigammainverse | Inverse Trigamma Function |
trimWhiteSpace | Trim Leading and Trailing White Space |
uniquegenelist | Eliminate Duplicate Names from the Gene List |
unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns |
venn | Venn Diagrams |
volcanoplot | Volcano Plot |
voom | Transform RNA-Seq Data Ready for Linear Modelling |
vooma | Convert Mean-Variance Trend to Observation-specific Precision... |
voomWithQualityWeights | Combining observational-level with sample-specific quality... |
weightedLowess | LOWESS Smoother with Prior Weights |
weightedmedian | Weighted Median |
writefit | Write MArrayLM Object to a File |
wsva | Weighted Surrogate Variable Analysis |
zscore | Transform non-normal random deviates to standard normal |
zscoreT | Transform t-statistics to standard normal |
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