Linear Models for Microarray Data

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 |

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 directly 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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