3.ReadingData {limma} | R Documentation |
This help page gives an overview of LIMMA functions used to read data into R from files.
The function readTargets
is designed to help with organizing information about which RNA sample is hybridized to each channel on each array and which files store information for each array.
The first step in a microarray data analysis is to read into R the intensity data for each array provided by an image analysis program.
This is done using the function read.maimages
.
read.maimages
optionally constructs quality weights for each spot using quality functions listed in QualityWeights.
read.maimages
produces an RGList
object and stores only the information required from each image analysis output file.
If you wish to read all the image analysis output files into R as individual data frames containing all the original columns, you may use read.series
.
An RGList
object can be extracted from the data frames at a later stage using the functions rg.spot
, rg.genepix
or rg.quantarray
.
Another function, rg.series.spot
is very similar to read.maimages
with source="spot"
.
This function will be removed in future versions of LIMMA.
Many image analysis program provide gene IDs as columns in the image analysis output files, for example ArrayVision, Imagene and the Stanford Microarray Database.
In other cases you may have gene name and annoation information in a separate file.
The function readGAL
reads information from a GenePix Allocation List (gal) file.
It produces a data frame with known column names.
If the gene names consist of a short name followed by annotation information, then splitName
may be used to separate the name and annotation information into separate vectors.
The functions readSpotTypes
and controlStatus
assist with separating control spots from ordinary genes in the analysis and data exploration.
The function getLayout
extracts from the gal-file data frame the print layout information for a spotted array.
The functions gridr
, gridc
, spotr
and spotc
use the extracted layout to compute grid positions and spot positions within each grid for each spot.
The function printorder
calculates the printorder, plate number and plate row and column position for each spot given information about the printing process.
The utility function getSpacing
converts character strings specifying spacings of duplicate spots to numeric values.
If each gene is printed more than once of the arrays, then uniquegenelist
will remove duplicate names from the gal-file or gene list.
cbind
allows different RGList
or MAList
objects to be combined assuming the layout of the arrays to be the same.
merge
can combine data even when the order of the genes on the arrays has changed.
merge
uses utility function makeUnique
.
Gordon Smyth