3.3 years ago by
For a simple experiment like that, you don't need a targets file, per se. You can just read the data in, and then use the resulting data.frame as input to
From the help page for
lmFit(object, design=NULL, ndups=1, spacing=1, block=NULL, correlation, weights=NULL,
object: A matrix-like data object containing log-ratios or
log-expression values for a series of arrays, with rows
corresponding to genes and columns to samples. Any type of
data object that can be processed by 'getEAWP' is acceptable.
And since this points us to
getEAWP, let's look at that:
object: any matrix-like object containing log-expression values. Can
be an object of class 'MAList', 'EList', 'marrayNorm',
'PLMset', 'vsn', or any class inheriting from
'ExpressionSet', or any object that can be coerced to a
Since a data.frame is an object that can be coerced to a numeric matrix, a data.frame is a suitable input. But do note that R has an unfortunate habit of converting things that it thinks should be factors into factors, if you have any non-numeric things in your input file, you may have to do some coercion of your own to make sure you have numeric values before
getEAWP converts to a matrix.