| AcceptFilter | The AcceptFilter class |
| addFlag.MicroarrayData | Flags or unflags the indices of some spots with a specific... |
| AffineModelFit | Model fit of affine microarray models |
| AFilter | FieldFilter for the log-intensities (A) |
| AndFilter | The AndFilter class |
| append.MicroarrayData | Appends another MicroarrayData object |
| aroma-package | Package aroma |
| as.character.SpotPosition | Gets a character represenation of the spot positions |
| as.data.frame.MicroarrayData | Converts the object to a data frame |
| as.data.frame.SpotPosition | Gets a data frame represenation of the spot positions |
| as.layout.SMA | Converts a aroma object into an object of the layout... |
| as.MAData.RGData | Transform from the red and green intensities into log ratios... |
| as.RGData.MAData | Transform MA format into RG format |
| as.RG.SMA | Converts a aroma object into an object of the RG structure |
| boxplot.MicroarrayData | Plots a boxplot |
| calibrateMultiscan.RGData | Calibrates multiple re-scanned images based on an affine... |
| changeInput.Filter | Change input(s) on this filter and optionally all filters... |
| changeInput.ParallelFilter | Replaces input filters with other ones |
| changeInput.SerialFilter | Change input(s) on this filter and optionally all filters... |
| clearFlag.MicroarrayData | Clears the spots from the specified flag |
| convertFieldNames.GenePixData | Convert field names that contains patterns |
| DfFilter | FieldFilter for the log-intensities (A) |
| equals.Layout | Checks if a Layout object is equals to some other object |
| equals.MicroarrayData | Compares a MicroarrayData object with another Object |
| estimateMACurve.MAData | Estimates a smooth intensity-dependent curve in (A,M) |
| ExperimentalSetup | The ExperimentalSetup class |
| extract.MicroarrayData | Gets a subset of data specified by fields, slides and/or spot... |
| FieldFilter | The FieldFilter class |
| Filter | The Filter class |
| findSetupFiles.ExperimentalSetup | Locates cDNA microarray experiment setup files |
| fitMultiscanAffine.RGData | Fits an affine model to signals from a multi-scanned slide |
| fromSaturatedSignals.SignalWeights | Weight function for scanner signals |
| GalLayout | Class representing GenePix Array List (GAL) data |
| GeneAcceptFilter | The GeneAcceptFilter class |
| GeneGroups | The GeneGroups class |
| GenePixData | The GenePixData class |
| GeneRejectFilter | The GeneRejectFilter class |
| getAdjustedSpotVariability.MAData | Gets the spotwise intensity-adjusted variability of replicate... |
| getArea.GenePixData | Gets the area of the spot |
| getAspectRatio.SpotPosition | Gets the aspect ratio of the spots |
| getBackground.RawData | Gets the background signal |
| getBackgroundSD.GenePixData | Gets the standard deviation of the background pixels |
| getBottomEdge.SpotPosition | Gets the y-coordinate of the spot at the very bottom |
| getChannelNames.GenePixData | Gets the names of the channels |
| getChannelNames.MicroarrayData | Gets the names of the channels |
| getColors.MAData | Generates colors for each of the specified spots |
| getColors.RawData | Generates colors for each of the specified spots |
| getColors.RGData | Generates red to green colors for each of the specified spots |
| getDistancesTo.SpotPosition | Gets the Euclidean distance from one spot to a set of other... |
| getDuplicates.GeneGroups | Gets all duplicated spots |
| getExtra.MicroarrayData | Gets an extra field |
| getFieldNames.MicroarrayData | Gets the names of all fields containing spot specific data |
| getFlag.MicroarrayData | Gets the indices of the spots flagged with a specific flag |
| getForeground.RawData | Gets the foreground signal |
| getForegroundSD.GenePixData | Gets the standard deviation of the foreground pixels |
| getForegroundSD.SpotData | Gets (an approximation of) the standard deviation of the... |
| getForegroundSE.GenePixData | Gets the standard error of the foreground pixels |
| getForegroundSE.SpotData | Gets the standard error of the foreground pixels |
| getGeneSlideReplicateIndex.MicroarrayData | Returns the index of the spots in (gene,slide,replicate)... |
| getGeneVariability.MAData | Gets the genewise variability |
| getId.Layout | Gets the id of one or more spots |
| getIndex.AcceptFilter | Gets indices accepted by this filter |
| getIndex.AndFilter | Gets indices accepted by this filter |
| getIndex.FieldFilter | Gets indices accepted by this filter |
| getIndex.Filter | Gets the indices accepted by the filter |
| getIndex.Layout | Gets the index of a spot given its location |
| getIndex.OrFilter | Gets indices accepted by this filter |
| getIndices.Layout | Gets the indices of the spots at the given locations |
| getInput.Filter | Gets all the input objects connected to the filter |
| getInput.ParallelFilter | Gets the input filters |
| getInput.SerialFilter | Gets all the input objects connected to the filter |
| getLabel.MicroarrayData | Gets the label of one field |
| getLayout.MicroarrayData | Gets the layout |
| getLeftEdge.SpotPosition | Gets the x-coordinate of the left most spot |
| getLocation.Layout | Gets the location of a spot given its index |
| getLogIntensities.RGData | Calculates the log-intensitites (A values) |
| getLogRatios.RGData | Calculates the log-ratios (M values) |
| getMaxHeight.SpotPosition | Gets the maximum y-distance between two spots |
| getMaxWidth.SpotPosition | Gets the maximum x-distance between two spots |
| getMOR2003a.MAData | Gets the Intensity Adjusted Measure of Reproducibility |
| getMOR.MAData | Gets the Measure of Reproducibility |
| getName.Layout | Gets the name of one or more spots |
| getNames.GeneGroups | Gets the names of the unique gene names |
| getParameter.Filter | Gets the values for a specific parameter for indices accepted... |
| getPosition.Layout | Gets the position of a set of spots given their indices |
| getPrintorder.Layout | Gets the order of the spots in which they were printed |
| getQuadruplicates.GeneGroups | Gets all quadruplicated spots |
| getRawData.GenePixData | Gets the raw intensites from the GPR structure |
| getRawData.ImaGeneData | Gets the raw intensites from two ImaGeneData objects |
| getRawData.QuantArrayData | Gets the raw intensites from the QuantArray data structure |
| getRawData.ScanAlyzeData | Gets the raw (foreground and background) intensites |
| getRawData.SpotData | Gets the raw intensites from the SpotData structure |
| getRawData.SpotfinderData | Gets the raw intensites from the SpotfinderData structure |
| getReplicates.GeneGroups | Gets all spots that exist with a certain number of replicates |
| getRightEdge.SpotPosition | Gets the x-coordinate of the right most spot |
| getSignal.RawData | Gets the red and the green signal |
| getSizes.GeneGroups | Gets the number of replicates for each gene |
| getSlideNames.MicroarrayData | Gets the names of the slides |
| getSpotPosition.GenePixData | Gets physical positions of the spots |
| getSpotPosition.ImaGeneData | Gets physical positions of the spots |
| getSpotPosition.QuantArrayData | Gets physical positions of the spots |
| getSpotPosition.ScanAlyze20Data | Gets physical positions of the spots |
| getSpotPosition.ScanAlyzeData | Gets physical positions of the spots |
| getSpotPosition.SpotData | Gets physical positions of the spots |
| getSpots.GeneGroups | Gets a list of items each containing spot indices for a group |
| getTopEdge.SpotPosition | Gets the y-coordinate of the spot at the very top |
| getTriplicates.GeneGroups | Gets all triplicated spots |
| getVisible.Filter | Checks if the filter is visible or not |
| gridSize.Layout | Gets the number of spots in each grid |
| hasLayout.MicroarrayData | Checks if the layout has been specified |
| highlight.Filter | Highlights the data points accepted by the filter |
| highlight.MicroarrayData | Highlight spots in last plot |
| hist.MicroarrayData | Plots a histogram |
| ImaGeneData | The ImaGeneData class |
| indexOf.Layout | Gets the index of one or more spots from their name or id |
| isSaturated.MicroarrayData | Check if some observations are saturated or not |
| keepSlides.MicroarrayData | Remove all but the specified slides |
| keepSpots.MicroarrayData | Remove all but the specified spots from all slides |
| Layout | The Layout class |
| LayoutGroups | The LayoutGroups class |
| listFlags.MicroarrayData | Lists the names of all known flags |
| loessQuantile.MAData | Estimates the (25%,50%,75%) quantile M(A) curves using loess |
| lowessCurve.MicroarrayData | Draws one or more lowess curves through the data in last plot |
| MAData | The MAData class |
| mean.MAData | Average Mean for microarray data |
| mean.RGData | Genewise Average Mean for channel R and G |
| MFilter | FieldFilter for the log-ratios (M) |
| MicroarrayData | The MicroarrayData class |
| nbrOfColumns.Layout | Gets the number of columns on a microarray |
| nbrOfFields.MicroarrayData | Gets the number of fields |
| nbrOfGrids.Layout | Gets the number of grids on a microarray |
| nbrOfGroups.GeneGroups | Gets the number of unique genes |
| nbrOfRows.Layout | Gets the number of rows on a microarray |
| nbrOfSlides.MicroarrayData | Gets the number of slides |
| nbrOfSlides.SpotPosition | Gets the number of slides |
| nbrOfSpots.Layout | Gets the size of a microarray |
| nbrOfSpots.MicroarrayData | Gets the number of spots in each of the slides |
| nbrOfSpots.SpotPosition | Gets the number of spots in each of the slides |
| Non-documented_objects | Non-documented objects |
| normalizeAcrossSlides.MAData | Normalizes across slides |
| normalizeAffine.MAData | Affine normalization based on non-logged data |
| normalizeAffine.RGData | Weighted affine normalization between channels and arrays |
| normalizeAffineShift.MAData | Within-slide normalization that adjust the channel bias |
| normalizeCurveFit.MAData | Within-slide normalization that adjust log-ratios by... |
| normalizeCurveFit.RGData | Within-slide intensity-dependent normalization in (A,M) |
| normalizeLogRatioShift.MAData | Within-slide normalization that adjust the log-ratios shift |
| normalizePlatewise.MicroarrayData | Normalization performed plate by plate |
| normalizeWithinSlide.MAData | Within-slide normalization |
| NotFilter | The NotFilter class |
| OrFilter | The OrFilter class |
| ParallelFilter | The ParallelFilter class |
| PlateGroups | The PlateGroups class |
| plotDensity.MicroarrayData | Plots the empirical density distribution of a field |
| plot.MicroarrayData | Plots spatial representation of a microarray spot statistics |
| plotMvsM.MAData | Plots the log-ratios for one slide versus another |
| plotPrintorder.MicroarrayData | Plots the data as a time series in the order it was printed |
| plotSpatial3d.MicroarrayData | Plots a 3-dimensional spatial representation of a field |
| plotSpatial.GenePixData | Creates a spatial plot of a slide |
| plotSpatial.MicroarrayData | Plots a spatial representation of one field |
| plotSpatial.QuantArrayData | Creates a spatial plot of a slide |
| plotSpatial.ScanAlyzeData | Creates a spatial plot of a slide |
| plotSpatial.SpotData | Creates a spatial plot of a slide |
| plotSpatial.SpotfinderData | Creates a spatial plot of a slide |
| plot.SpotPosition | Plots the spot positions in an xy scatter plot |
| plotXY.MicroarrayData | Plots a scatter plot of two fields |
| points.SpotPosition | Adds spot positions to an existing plot |
| PrintdipGroups | The PrintdipGroups class |
| PrinttipGroups | The PrinttipGroups class |
| QuantArrayData | The QuantArrayData class |
| RawData | The RawData class |
| read.ExperimentalSetup | Reads a file specifying the setup of a microarray experiment |
| read.GalLayout | Reads a GenePix Array List (GAL) file |
| read.GenePixData | Reads one or several GenePix files into one GenePixData... |
| readHeader.GenePixData | Reads a GenePix Results (GPR) file header |
| read.ImaGeneData | Reads an ImaGene result file |
| read.Layout | Reads layout information from a tab-delimited file |
| read.MicroarrayData | Reads microarray data generated by another software package |
| readOneFile.QuantArrayData | Reads a QuantArray result file |
| readOneFile.SpotfinderData | Reads TAV files generated by Spotfinder |
| read.QuantArrayData | Reads one or several QuantArray files into one QuantArrayData... |
| read.ScanAlyze20Data | Reads one or several ScanAlyze v2.0 files |
| read.ScanAlyzeData | Reads one or several ScanAlyze files into a ScanAlyzeData... |
| read.SpotData | Reads several Spot files into a SpotData object |
| read.SpotfinderData | Reads several Spotfinder/TAV files into a SpotfinderData... |
| RejectFilter | The RejectFilter class |
| removeSlides.MicroarrayData | Remove specified slides |
| removeSpots.MicroarrayData | Remove specified spots |
| RGData | The RGData class |
| ScanAlyze20Data | The ScanAlyze20Data (ScanAlyze v2.0) class |
| ScanAlyzeData | The ScanAlyzeData class |
| SEFilter | FieldFilter for the log-intensities (A) |
| select.MicroarrayData | Selects rows with certain criteria |
| SerialFilter | The SerialFilter class |
| setExtra.MicroarrayData | Sets an extra field |
| setFlag.MicroarrayData | Sets the flags on some of the spots |
| setId.Layout | Sets the id of one or more spots |
| setLabel.MicroarrayData | Sets the label of one field |
| set.Layout | Sets the layout |
| setLayout.MicroarrayData | Sets the layout |
| setName.Layout | Sets the name of one or more spots |
| setParameter.Filter | Sets the values for a specific parameter for indices accepted... |
| setProbeWeights.MicroarrayData | Sets probe weights on one or several slides |
| setSaturated.MicroarrayData | Set which observations in a given channel that are saturated... |
| setSlideNames.MicroarrayData | Sets the names of the slides |
| setVisible.Filter | Sets if the filter should bee visible or not |
| shift.MAData | Shift the log-ratios, log-intensities or the raw signal |
| shift.RawData | Shift the log-ratios, log-intensities or the raw signal |
| shift.RGData | Shift the log-ratios, log-intensities or the raw signal |
| size.Layout | Gets the size of a microarray |
| size.MicroarrayData | Gets the number of spots in all slides together |
| size.SpotPosition | Gets the number of spots in all slides together |
| SlideColumnGroups | The SlideColumnGroups class |
| SlideRowGroups | The SlideRowGroups class |
| SMA | The SMA class |
| SpotData | The SpotData class |
| SpotfinderData | The SpotfinderData class |
| SpotPosition | Class representing spot positions |
| str.MicroarrayData | Compactly Display the Structure of a MicroarrayData object |
| subplots.MicroarrayData | Prepare for a grid of subplots based on the number of slides |
| summary.MicroarrayData | Gets summary statistics for the fields |
| swapDyes.MAData | Dye swap one or many slides |
| swapDyes.RawData | Dye swap one or many slides |
| swapDyes.RGData | Swap dyes of one or many slides |
| text.Filter | Labels the data points accepted by the filter |
| text.MicroarrayData | Puts labels to the spots in last plot |
| toPrintorderMatrix.Layout | Gets a matrix of spot indices in the order they were printed |
| topSpots.MAData | Gets the top spots |
| toXYMatrix.Layout | Layouts out values in the same way as the spots are layout |
| unite.MicroarrayWeights | Coalesce weights of lower order into higher order weights |
| validateArgumentChannels.GenePixData | Validates the argument 'channels' |
| validateArgumentGroupBy.MicroarrayData | Validates the argument 'groupBy' |
| validateArgumentSlide.MicroarrayData | Validates the argument 'slide' |
| validateArgumentSlides.MicroarrayData | Validates the argument 'slides' |
| validateArgumentWeights.MicroarrayData | Validates the argument 'weights' |
| var.MAData | Variance for microarray data |
| var.RGData | Genewise Variance for channel R and G |
| Weights | Weights |
| write.GenePixData | Write a GenePix Results Data file |
| write.ImaGeneData | Write an ImaGene result data file |
| write.Layout | Writes the layout information to a tab-delimited file |
| write.MicroarrayData | Write a MicroarrayData object to file |
| write.QuantArrayData | Write a QuantArray result data file |
| write.ScanAlyze20Data | Writes a ScanAlyze v2.0 Results Data file (NOT IMPLEMENTED) |
| write.ScanAlyzeData | Write a ScanAlyze Results Data file |
| write.SpotData | Write a SpotData object to file |
| write.SpotfinderData | Write a SpotfinderData object to file |
| write.SpotPosition | Write a SpotPosition object to file |
