contrast_the_group_to_the_rest_with_limma_for_microarray: contrast_the_group_to_the_rest_with_limma_for_microarray

In MonashBioinformaticsPlatform/celaref: Single-cell RNAseq cell cluster labelling by reference

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.

MonashBioinformaticsPlatform/celaref documentation built on June 5, 2019, 11:35 a.m.