| agilent.miRNA.cbind | cbind Agilent miRNA datasets Combine 2 Agilent miRNA objects... |
| agilent.miRNA.filter.GX10 | Filter Agilent miRNA data Keep only the miRNA's that start... |
| agilent.miRNA.normalise.GX10 | Normalise Agilent miRNA data Normalise an Agilent miRNA data... |
| agilent.miRNA.preprocess | Preprocess Agilent miRNA data. From a table of imported... |
| agilent.miRNA.preprocess.GX10 | Preprocess Agilent miRNA data Preprocess raw Agilent data,... |
| agilent.miRNA.threshold.GX10 | Threshold Agilent miRNA data Threshold raw Agilent miRNA data... |
| as.data.frame.AnnotatedDataFrame | Coerce to a Data Frame |
| average.pval.replicates-methods | average.pval.replicates |
| average.replicates-methods | Average replicate columns |
| barplot_lmFit | Multipanel barplot of results from an lmFit |
| blatGene | Affy probe sequences to BLAT input |
| calc.best.probe.topTable | From a toptable which contains probe ID's in the ID column,... |
| catplot.RankProd | CAT plot comparing N RankProd analyses. |
| collapse-methods | collapse |
| collapse.topTable | Take a topTable with one row per probeset, and collapse it to... |
| controlDataSetter-methods | replace the controlData slot in a LumiBatch object |
| convert.partek2topTable | Convert Partek to topTable Convert a toptable made by... |
| DEgenes.topTable | Get the DE genes from a topTable. Get the lists of DE genes... |
| DetectionCalls-methods | DetectionCalls |
| dotplot-methods | dotplots on ExpressionSet objects |
| export.DEgenes.topTable | Export the DE genes from a topTable. Get the DE genes passing... |
| export.gsea.rnk.RankProd | Take the results from a RankProd analysis, and produce a rnk... |
| export.topTable | Export a topTable, or a list of top tables to an excel file.... |
| ExtractionSoftware-methods | ExtractionSoftware |
| hist_pvals_pi0 | histrogram of p-values |
| import.agilent | Import an Agilent result file |
| import.agilent.column2table | Extract a column from Agilent files. Take a vector of... |
| import.Agilent.GeneView.Experiment | Import a collection of GeneView files |
| import.Agilent.GeneView.File | Import Agilent GeneView files |
| import.illumina.bgx | Import an Illumina microarray manifest file. |
| is.topTable.list | Is the argument a single topTable, or a list of topTables |
| logFC2signedFC | Convert logFC (FoldChange) to signed FC When logFC<0,... |
| lowessMA | add a lowess curve to a plot created by plotMA |
| LumiBatch2gct | convert a LumiBatch to a GCT object |
| LumiBatch2GEOarchive | Convert a LumiBatch into a GEOarchive formatted file |
| make.sample.info.Agilent | Autocreate sample.info from Agilent filenames From a vector... |
| merge_topTable | Function to merge N topTable's together, retaining a... |
| mget2 | enhanced mget |
| mget.chain | Lookup keys in a chain of 2 environment or AnnDbBimap objects |
| mget.multi | mget with multiple search keys |
| microarrays-package | mjc's microarrays package |
| normalizeQuantiles.list | Function to qnorm a list of matrices It joins the list... |
| plot_arrayWeights | Plot array weights |
| plot_cor_topTable | Compare two topTables via correlation of the t-stats |
| plot_dabg_vs_rma | Density plot of DABG vs expression levels Plot the RMA... |
| plot_exprs_vs_detection-methods | plot_exprs_vs_detection |
| plot_genespringGX_lines | Perform a GeneSpring GX 7.3.1 line plot |
| plot_lumi_QC_all | Perform all of the QC plots that are mentioned in the lumi... |
| plotMA.all | Make N MAplots, writing out files into a directory. |
| plot_venn2D_topTable | Venn Diagram from 2 topTable objects Plot a Venn Diagram of... |
| plot_venn3D_topTable | Venn Diagram from 3 topTable objects Plot a Venn Diagram of... |
| RankProd.signed.score | From the results of a RankProd analysis, create a signed... |
| round.topTable | Round the numeric columns in a topTable Take a top table, and... |
| sampleNamesSetter-methods | set sampleNames in LumiBatch objects |
| sort-methods | sort ExpressionSet and LumiBatch objects |
| subset.eSet | subset an eSet object |
| subset-LumiBatch-methods | subset a LumiBatch object |
| subset.MArrayLM | Subset an MArrayLM object. |
| summarise.dabg | Sumarise an Affymetrix DABG file The Detected Above... |
| summarise.topTable | Summarise a topTable object |
| summarise.topTable.list | Summarise a list of topTables. |
| summarise.topTable.updown | Summarise a toptable into the up/down regulated genes |
| topTable.all | Run topTable on all contrasts from a linear model fit... |
| topTable.fixFC | 'fix' the logFC column for biologists (sorry!) |
| topTable.SE | Add a moderated SE column to a topTable object. |
| topTable.to.label | Take a toptable (Fstat or t-stat) and make a label for each... |
| transform_Agilent_log | Log transform and offset of Agilent data. |
| volcanoplot_topTable | A topTable volcano plot. Volcano plot of a toptable - similar... |
| volcanoplot_topTable_PandQ | A wrapper function to plot 2 volcano plots side by side, for... |
