Package: marray 1.85.0
Yee Hwa (Jean) Yang
marray: Exploratory analysis for two-color spotted microarray data
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
Authors:
marray_1.85.0.tar.gz
marray_1.85.0.zip(r-4.5)marray_1.85.0.zip(r-4.4)marray_1.85.0.zip(r-4.3)
marray_1.85.0.tgz(r-4.4-any)marray_1.85.0.tgz(r-4.3-any)
marray_1.85.0.tar.gz(r-4.5-noble)marray_1.85.0.tar.gz(r-4.4-noble)
marray_1.85.0.tgz(r-4.4-emscripten)marray_1.85.0.tgz(r-4.3-emscripten)
marray.pdf |marray.html✨
marray/json (API)
| # Install 'marray' in R: |
| install.packages('marray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- swirl - Gene expression data from Swirl zebrafish cDNA microarray experiment
On BioConductor:marray-1.85.0(bioc 3.21)marray-1.84.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraytwochannelpreprocessing
Last updated 2 months agofrom:a8c55f65e4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | NOTE | Dec 19 2024 |
Exports:addLinesaddPointsaddTextboxplotcbind.marrayNormcbind.marrayRawcheckTargetInfocoercecontrolCodecor.nafindIDhtmlPageimagelength.nalineslog.nama2DmaAmaA<-maBoxplotmaColorBarmaCompCoordmaCompIndmaCompLayoutmaCompNormAmaCompNormEqmaCompPlatemaControlsmaControls<-maCoord2IndmaDefaultParmaDotsDefaultsmaDotsMatchmaGbmaGb<-maGenControlsmaGeneTablemaGfmaGf<-maGnamesmaGnames<-maGridColmaGridRowmaImagemaImage.funcmaInd2CoordmaInfomaInfo<-maLabelsmaLabels<-maLayoutmaLayout<-maLegendLinesmaLGmaLoessmaLoessLinesmaLowessLinesmaLRmaMmaM<-maMADmaMedmaMlocmaMloc<-maMscalemaMscale<-maNgcmaNgc<-maNgrmaNgr<-maNormmaNorm2DmaNormCallmaNormLoessmaNormMADmaNormMainmaNormMedmaNormScalemaNotesmaNotes<-maNsamplesmaNscmaNsc<-maNspotsmaNspots<-maNsrmaNsr<-maNum2LogicmaPalettemapGeneInfomaPlatemaPlate<-maPlotmaPlot.funcmaPrintTipmaRbmaRb<-maRfmaRf<-maSelectGnamesmaSpotColmaSpotRowmaSubmaTargetsmaTargets<-maTextmaTopmaTwoSamplesmaWmaW<-mean.naopVersionIDorder.naplot.marrayNormplot.marrayRawpointsprod.naquantile.narbind.marrayInforead.Agilentread.fnameread.Galfileread.GenePixread.marrayInforead.marrayLayoutread.marrayRawread.SMDread.Spotrm.nascale.nashowstat.confband.textstat.gnamessum.nasummarytable2htmltextURLstringvar.nawidget.mapGeneInfowidget.marrayInfowidget.marrayLayoutwidget.marrayRawwidget.TwoSampleswrite.listwrite.marraywrite.xls
marray Normalization
Rendered frommarrayNorm.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
marray Overview
Rendered frommarray.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
marrayClasses Overview
Rendered frommarrayClasses.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
marrayClasses Tutorial (short)
Rendered frommarrayClassesShort.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
marrayInput Introduction
Rendered frommarrayInput.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
marrayPlots Overview
Rendered frommarrayPlots.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2013-11-01
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Subsetting methods for microarray objects | [ [-methods |
| Boxplots for cDNA microarray spot statistics | boxplot,marrayNorm-method boxplot,marrayRaw-method |
| Combine marrayRaw, marrayNorm or marrayInfo Objects | cbind.marrayNorm cbind.marrayRaw rbind.marrayInfo |
| Verifying the order between intensities matrix and target file information | checkTargetInfo |
| Coerce an object to belong to a given microarray class | as coerce coerce-methods |
| Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object | dim.marrayInfo dim.marrayNorm dim.marrayRaw |
| Find ID when given an accession number | findID |
| Display gene list as a HTML page | htmlPage table2html |
| Color image for cDNA microarray spot statistics | image,marrayNorm-method image,marrayRaw-method |
| Internal marray functions | gsubAnchor plot.gene.cluster read.fname stat.gene.cluster tablegen |
| Stratified bivariate robust local regression | ma2D |
| Boxplots for cDNA microarray spot statistics | maBoxplot |
| Calibration bar for color images | maColorBar |
| Generate grid and spot matrix coordinates | maCompCoord |
| Generate spot indices | maCompInd |
| Generate a marrayLayout object | maCompLayout |
| Weights for composite normalization | maCompNormA maCompNormEq |
| Generate plate IDs | maCompPlate |
| Convert grid and spot matrix coordinates to spot indices | maCoord2Ind |
| Default graphical parameters for microarray objects | maDefaultPar |
| Replace graphical default parameters by user supplied parameters | maDotsDefaults |
| Replace default arguments of a function by user supplied values | maDotsMatch |
| Generating a vector recording the control status of the spotted probe sequences. | controlCode maGenControls |
| Table of spot coordinates and gene names | maGeneTable |
| Color image for cDNA microarray spot statistics | maImage |
| Color image for cDNA microarray spot statistics | maImage.func |
| Convert spot indices to grid and spot matrix coordinates | maInd2Coord |
| Add a legend to a plot | maLegendLines |
| Stratified univariate robust local regression | maLoess |
| Add smoothed fits to a plot | maLoessLines maLowessLines |
| Stratified MAD calculation | maMAD |
| Stratified median calculation | maMed |
| Simple location and scale normalization function | maNorm |
| 2D spatial location normalization function | maNorm2D |
| Intensity dependent location normalization function | maNormLoess |
| MAD scale normalization function | maNormMAD |
| Main function for location and scale normalization of cDNA microarray data | maNormMain |
| Median location normalization function | maNormMed |
| Simple scale normalization function | maNormScale |
| Convert a numeric vector of indices to a logical vector | maNum2Logic |
| Microarray color palette | maPalette |
| Creating URL strings for external database links | mapGeneInfo SFGL UCBFGL URLstring widget.mapGeneInfo |
| Scatter-plots for cDNA microarray spot statistics | maPlot |
| Scatter-plots with fitted curves and text | maPlot.func |
| Class "marrayInfo", description of target samples or spotted probe sequences | maGnames<-,marrayNorm,marrayInfo-method maGnames<-,marrayRaw,marrayInfo-method maGnames<-,marraySpots,marrayInfo-method maInfo maInfo,marrayInfo-method maInfo<- maInfo<-,marrayInfo,data.frame-method maLabels maLabels,marrayInfo-method maLabels<- maLabels<-,marrayInfo,character-method maLabels<-,marrayInfo,numeric-method maNotes maNotes,marrayInfo-method maNotes<- maNotes<-,marrayInfo,character-method marrayInfo marrayInfo-class maTargets<-,marrayNorm,marrayInfo-method maTargets<-,marrayRaw,marrayInfo-method print,marrayInfo-method rbind,marrayInfo-method summary,marrayInfo-method [,marrayInfo-method |
| Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays | maControls maControls,marrayLayout-method maControls<- maControls<-,marrayLayout-method maGridCol maGridCol,marrayLayout-method maGridRow maGridRow,marrayLayout-method maLayout<-,marrayNorm,marrayLayout-method maLayout<-,marrayRaw,marrayLayout-method maNgc maNgc,marrayLayout-method maNgc<- maNgc<-,marrayLayout,numeric-method maNgr maNgr,marrayLayout-method maNgr<- maNgr<-,marrayLayout,numeric-method maNotes,marrayLayout-method maNotes<-,marrayLayout,character-method maNsc maNsc,marrayLayout-method maNsc<- maNsc<-,marrayLayout,numeric-method maNspots maNspots,marrayLayout-method maNspots<- maNspots<-,marrayLayout,numeric-method maNsr maNsr,marrayLayout-method maNsr<- maNsr<-,marrayLayout,numeric-method maPlate maPlate,marrayLayout-method maPlate<- maPlate<-,marrayLayout-method maPrintTip maPrintTip,marrayLayout-method marrayLayout marrayLayout-class maSpotCol maSpotCol,marrayLayout-method maSpotRow maSpotRow,marrayLayout-method maSub maSub,marrayLayout-method maSub<- maSub<-,marrayLayout,logical-method maSub<-,marrayLayout,numeric-method print,marrayLayout-method summary,marrayLayout-method [,marrayLayout-method |
| Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data | cbind,marrayNorm-method coerce,marrayRaw,marrayNorm-method maA maA,marrayNorm-method maA<- maA<-,marrayNorm,matrix-method maControls,marrayNorm-method maControls<-,marrayNorm-method maGnames,marrayNorm-method maGridCol,marrayNorm-method maGridRow,marrayNorm-method maLayout,marrayNorm-method maLG,marrayNorm-method maLR,marrayNorm-method maM maM,marrayNorm-method maM<- maM<-,marrayNorm,matrix-method maMloc maMloc,marrayNorm-method maMloc<- maMloc<-,marrayNorm,matrix-method maMscale maMscale,marrayNorm-method maMscale<- maMscale<-,marrayNorm,matrix-method maNgc,marrayNorm-method maNgc<-,marrayNorm,numeric-method maNgr,marrayNorm-method maNgr<-,marrayNorm,numeric-method maNormCall maNormCall,marrayNorm-method maNotes,marrayNorm-method maNotes<-,marrayNorm,character-method maNsamples,marrayNorm-method maNsc,marrayNorm-method maNsc<-,marrayNorm,numeric-method maNspots,marrayNorm-method maNspots<-,marrayNorm,numeric-method maNsr,marrayNorm-method maNsr<-,marrayNorm,numeric-method maPlate,marrayNorm-method maPlate<-,marrayNorm-method maPrintTip,marrayNorm-method marrayNorm marrayNorm-class maSpotCol,marrayNorm-method maSpotRow,marrayNorm-method maSub,marrayNorm-method maSub<-,marrayNorm-method maTargets,marrayNorm-method maW,marrayNorm-method maW<-,marrayNorm,matrix-method print,marrayNorm-method show,marrayNorm-method summary,marrayNorm-method [,marrayNorm-method |
| Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data | cbind,marrayRaw-method maA,marrayRaw-method maControls,marrayRaw-method maControls<-,marrayRaw-method maGb maGb,marrayRaw-method maGb<- maGb<-,marrayRaw,matrix-method maGb<-,marrayRaw,NULL-method maGf maGf,marrayRaw-method maGf<- maGf<-,marrayRaw,matrix-method maGnames maGnames,marrayRaw-method maGnames<- maGridCol,marrayRaw-method maGridRow,marrayRaw-method maLayout maLayout,marrayRaw-method maLayout<- maLG maLG,marrayRaw-method maLR maLR,marrayRaw-method maM,marrayRaw-method maNgc,marrayRaw-method maNgc<-,marrayRaw,numeric-method maNgr,marrayRaw-method maNgr<-,marrayRaw,numeric-method maNotes,marrayRaw-method maNotes<-,marrayRaw,character-method maNsamples maNsamples,marrayRaw-method maNsc,marrayRaw-method maNsc<-,marrayRaw,numeric-method maNspots,marrayRaw-method maNspots<-,marrayRaw,numeric-method maNsr,marrayRaw-method maNsr<-,marrayRaw,numeric-method maPlate,marrayRaw-method maPlate<-,marrayRaw-method maPrintTip,marrayRaw-method maRb maRb,marrayRaw-method maRb<- maRb<-,marrayRaw,matrix-method maRb<-,marrayRaw,NULL-method maRf maRf,marrayRaw-method maRf<- maRf<-,marrayRaw,matrix-method marrayRaw marrayRaw-class maSpotCol,marrayRaw-method maSpotRow,marrayRaw-method maSub,marrayRaw-method maSub<-,marrayRaw-method maTargets maTargets,marrayRaw-method maTargets<- maW maW,marrayRaw-method maW<- maW<-,marrayRaw,matrix-method print,marrayRaw-method show,marrayRaw-method summary,marrayRaw-method [,marrayRaw-method |
| Select genes according to the values of a few different statistics | maSelectGnames |
| Highlight points on a plot | maText |
| Identify extreme values | maTop |
| Changing signs for two sample analysis | maTwoSamples widget.TwoSamples |
| Basic Statistical Functions for Handling Missing Values | cor.na length.na log.na mean.na order.na prod.na quantile.na scale.na sum.na var.na |
| Determine the operon oligo set ID | opVersionID |
| Scatter-plots for cDNA microarray spot statistics | addLines addPoints addText lines,marrayNorm-method lines,marrayRaw-method plot.marrayNorm plot.marrayRaw points,marrayNorm-method points,marrayRaw-method text,marrayNorm-method text,marrayRaw-method |
| Reading GenePix Gal file | read.Galfile |
| Create objects of class marrayInfo | read.marrayInfo widget.marrayInfo |
| Create objects of class marrayLayout | read.marrayLayout widget.marrayLayout |
| Create objects of class "marrayRaw" | read.Agilent read.GenePix read.marrayRaw read.SMD read.Spot widget.marrayRaw |
| Remove missing values | rm.na |
| Show Large Data Object - class | show,ShowLargeObject-method ShowLargeObject-class |
| Rank genes according to the value of a statistic. | stat.confband.text |
| Sort Genes According to the Value of a Statistic | stat.gnames |
| Printing summary methods for microarray objects | summary-methods |
| Gene expression data from Swirl zebrafish cDNA microarray experiment | fish.gal swirl swirl.1.spot swirl.2.spot swirl.3.spot swirl.4.spot SwirlSample SwirlSample.txt |
| Data Output | write.list |
| Data Output | write.marray |
| Data Output | write.xls |