Package 'limma' - Bioconductor
Package 'limma' - Bioconductor
Package 'limma' - Bioconductor
You also want an ePaper? Increase the reach of your titles
YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.
6 02.Classes<br />
See Also<br />
02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel,<br />
08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq<br />
02.Classes<br />
Topic: Classes Defined by this <strong>Package</strong><br />
Description<br />
This package defines the following data classes.<br />
RGList A class used to store raw intensities as they are read in from an image analysis output file,<br />
usually by read.maimages.<br />
MAList Intensities converted to M-values and A-values, i.e., to with-spot and whole-spot contrasts<br />
on the log-scale. Usually created from an RGList using MA.RG or normalizeWithinArrays.<br />
Objects of this class contain one row for each spot. There may be more than one spot and<br />
therefore more than one row for each probe.<br />
EListRaw A class to store raw intensities for one-channel microarray data. May or may not be<br />
background corrected. Usually created by read.maimages.<br />
EList A class to store normalized log2 expression values for one-channel microarray data. Usually<br />
created by normalizeBetweenArrays.<br />
MArrayLM Store the result of fitting gene-wise linear models to the normalized intensities or logratios.<br />
Usually created by lmFit. Objects of this class normally contain only one row for each<br />
unique probe.<br />
TestResults Store the results of testing a set of contrasts equal to zero for each probe. Usually<br />
created by decideTests. Objects of this class normally contain one row for each unique<br />
probe.<br />
All these data classes obey many analogies with matrices. In the case of RGList, MAList, EListRaw<br />
and EList, rows correspond to spots or probes and columns to arrays. In the case of MarrayLM, rows<br />
correspond to unique probes and the columns to parameters or contrasts. The functions summary,<br />
dim, length, ncol, nrow, dimnames, rownames, colnames have methods for these classes. Objects<br />
of any of these classes may be subsetted. Multiple data objects may be combined by rows (to add<br />
extra probes) or by columns (to add extra arrays).<br />
Furthermore all of these classes may be coerced to actually be of class matrix using as.matrix,<br />
although this entails loss of information. Fitted model objects of class MArrayLM can be coerced to<br />
class data.frame using as.data.frame.<br />
The first three classes belong to the virtual class LargeDataObject. A show method is defined for<br />
LargeDataOjects which uses the utility function printHead.<br />
Author(s)<br />
Gordon Smyth
Change language