Man pages for axelmuller/geometric2
NURSA annotation aid
| datasetsAnnotation | dataset annotation |
| fitting | runs limma's lmFit, contrast.fit, and eBayes in succession |
| geneAnnotateGPL | get genes from gpl soft file Annotation with GPL requires... |
| get_contrast.matrix | create a contrast.matrix to be used with limma's fit function |
| get_design | create limma design object based on groups in a table called... |
| get_DSinfo | use GEOmetadb to get metadata for dataset |
| get_eset | create an ExpressionSet for a series matrix file |
| get_eset_from_table | cretes an ExpressionSet from a customized series matrix file |
| get_fitfiles | Get paths for limma output files |
| get_input | use part from step1 to get basic information needed to get... |
| get_input_only | use part from step1 to get basic information needed to get... |
| groups | assign groups |
| groups_and_contrasts | assign groups and create contrast file |
| hello | Hello, World! |
| limma_fit | Run limma on output of Step3 |
| process_fitoutput | add gene annotation from a reannotation package to limma... |
| process_fitoutput_with_gpl | add gene annotation from a gpl-soft-file to limma output |
| qc_plots | boxplots of GSMs |
| step_1 | Annotation Step 1 |
| write_fit_file | writes the result of the fitting() function to a text file. |
