contrast_the_group_to_the_rest_with_limma_for_microarray {celaref} | R Documentation

## contrast_the_group_to_the_rest_with_limma_for_microarray

### Description

Private function used by contrast_each_group_to_the_rest_for_norm_ma_with_limma

### Usage

      contrast_the_group_to_the_rest_with_limma_for_microarray(norm_expression_table,
      sample_sheet_table, the_group, sample_name, extra_factor_name = NA,
      pval_threshold = 0.01)

### Arguments

`norm_expression_table` | A logged, normalised expression table. Any filtering (removal of low-expression probes/genes)
`sample_sheet_table` | Tab-separated text file of sample information. Columns must have names. Sample/microarray ids should be listed under sample_name column. The cell-type (or 'group') of each sample should be listed under a column group_name.
`the_group` | Which query group is being tested.
`sample_name` | Name of sample_sheet_table with sample ID
`extra_factor_name` | Optionally, an extra cross-group factor (as column name in sample_sheet_table) to include in the model used by limma. E.g. An individual/mouse id. Refer limma docs. Default = NA
`pval_threshold` | For reporting only, a p-value threshold. Default = 0.01

### Value

A tibble, the within-experiment de_table (differential expression table), for the group specified.

### See Also

`contrast_each_group_to_the_rest_for_norm_ma_with_limma` public calling function

Limma Limma package for differential expression.

[Package celaref version 1.12.0 Index]