Read and process microarray data using the limma package

The function reads in the microarray data, removes the control probes, performs background correction, normalization, and averages over irregular replicate probes (avereps)

process_microarr_dta_limma(
  micro_arr_path,
  micro_arr_source = "agilent",
  green.only = TRUE,
  backg_corr_meth = "normexp",
  back_corr_offset = 16,
  norm_arrays_meth = "quantile",
  ID_used = "GeneName"
)

Arguments

micro_arr_path

String indicating the path to a folder containing all and only microrna text

micro_arr_source

The source of the microarray data. Choices can be seen using limma documentation for the function read.maimages

green.only

Boolean for the green only parameter of read.maimages

backg_corr_meth

The background correction method with backgroundCorrect

back_corr_offset

The offset integer to use with backgroundCorrect

norm_arrays_meth

The normalization method to use with normalizeBetweenArrays

ID_used

The gene IDs used for the Elist. The name given must match a column in the 'genes' dataframe of the data. If set to NULL, the first column is taken

Value

The processed and normalized Elist object