Man pages for ammar257ammar/ArrayAnalysis-Bioconductor
ArrayAnalysis
| addStandardCDFenv | Check that a cdf environment is loaded |
| addUpdatedCDFenv | Load an updated cdf environment from BrainArray |
| array.image | Create several types of spatial images |
| backgroundPlot | Create an image of the background intensities and deviations |
| boxplotFun | Create an image with intensity boxplots for all arrays |
| clusterFun | Create a hierarchical clustering dendrogam |
| colorsByFactor | Create colors for the plots and the legends |
| computeAdvancedStatistics | Compute more advanced statistics |
| computePMAtable | Prepare and return a table of PMA calls |
| computeStatistics | Compute the statistics |
| controlPlots | Create an image of the scale factors of the array |
| correlFun | Create an image of the intensity correlation values |
| coverAndKeyPlot | Plot a cover sheet |
| createCutOffTab | For each comparison, create a cutoff table (P-value, LogFC... |
| createFCHist | For each comparison table, create a Fold Change histogram... |
| createNormDataTable | Prepare and export the normalized data table |
| createPvalHist | For each comparison table, create a P-value histogram plot |
| createPvalTab | Create significant pvalue table |
| createVennPlot | create a venn diagram plot |
| createVolcanoPlot | create a volcano plot |
| deduceSpecies | Find the species of the chiptype |
| defaultMatrix | Default comparison (for less than 5 experimental factors) |
| densityFun | Create an image with a density curve of the intensities |
| densityFunUnsmoothed | Create an image with an unsmoothed density curve of the... |
| enterMatrix | Advanced comparison: enter custom contrasts |
| getArrayType | Determine array type used |
| hybridPlot | Create an image of hybridisation controls |
| maFun | Create MA plots for each array versus the median array for... |
| normalizeData | Normalize the data set |
| nuseFun | Create an image with boxplots of normalized Unscaled Standard... |
| pcaFun | Create a Principal Component Analysis (PCA) plot |
| percPresPlot | Creates an image of the percentage present values of each... |
| plotArrayLayout | Create an image of the layout of the current chiptype |
| PNdistrPlot | Create an image with boxplots of positive and negative... |
| PNposPlot | Create an image showing the centres of intensity of the... |
| QCtablePlot | Compute and plot a table of QC statistics |
| ratioPlot | Create an image of beta-actin and GAPDH 3'/5' ratios |
| readDescFile | Read desc file. Return array names and groups |
| readExtFile | Read norm file, depending on the file type (supports: txt,... |
| rleFun | Create an image with boxplots of Relative Log Expression... |
| RNAdegPlot | Creates an image of overall RNA degradation for all arrays |
| samplePrepPlot | Create an image of sample preparation controls |
| saveComparison | For each contrast, save the comparison into files |
| scaleFactPlot | Create an image of the scale factors of the array |
| spatialImages | Create an image per array, containing one to four spatial... |
| toptable | Create a toptable and save it into a file |
