This help page gives an overview of LIMMA functions used to read data from files.
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 optionally constructs quality weights for each spot using quality functions listed in QualityWeights.
If the data is two-color, then
read.maimages produces an
If the data is one-color (single channel) then an
EListRaw object is produced.
In either case,
read.maimages stores only the information required from each image analysis output file.
read.maimages uses utility functions
There are also a series of utility functions which read the header information from image output files including
read.ilmn reads probe or gene summary profile files from Illumina BeadChips,
and produces an
read.idat reads Illumina files in IDAT format, and produces an
detectionPValues can be used to add detection p-values.
The function as.MAList can be used to convert a
marrayNorm object to an
MAList object if the data was read and normalized using the marray and marrayNorm packages.
Most image analysis software programs provide gene IDs as part of the intensity output files, for example GenePix, Imagene and the Stanford Microarray Database do this.
In other cases the probe ID and annotation information may be in a separate file.
The most common format for the probe annotation file is the GenePix Array List (GAL) file format.
readGAL reads information from a GAL file and produces a data frame with standard column names.
getLayout extracts from the GAL-file data frame the print layout information for a spotted array.
spotc use the extracted layout to compute grid positions and spot positions within each grid for each spot.
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.
The Australian Genome Research Facility in Australia often produces GAL files with composite probe IDs or names consisting of multiple strings separated by a delimiter.
These can be separated into name and annotation information using
If each probe is printed more than once of the arrays in a regular pattern, then
uniquegenelist will remove duplicate names from the gal-file or gene list.
controlStatus assist with separating control spots from ordinary genes in the analysis and data exploration.
merge allow different
MAList objects to be combined.
cbind combines data from different arrays assuming the layout of the arrays to be the same.
merge can combine data even when the order of the probes on the arrays has changed.
merge uses utility function
01.Introduction, 02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel, 08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq
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