[BioC] limma toptable output
wettenhall at wehi.edu.au
Fri Nov 7 03:26:05 MET 2003
The lmFit function calculates an average log intensity (A)
across the arrays (from MA$A) and this is then stored within the
fit object (as fit$Amean). The fit object passed to topTable
contains a number of useful attributes. Try typing
By typing "topTable", you can see the R code for this function
which calls the toptable function, with A = fit$Amean.
Similarly, typing "lmFit", shows:
fit$Amean <- rowMeans(unwrapdups(as.matrix(object$A),
ndups = ndups, spacing = spacing), na.rm = TRUE)
You can use names(fit) to check the names of the attributes
in the fit object.
On Thu, 6 Nov 2003, Dick Beyer wrote:
> In the limma manual, 27 October 2003, near the bottom of page 3, the output from the command
> topTable(fit, n=30, adjust="fdr")
> shows a column "A".
> Block Row Column ID Name M A t P.Value B
> 3721 8 2 1 control BMP2 -2.21 12.1 -21.1 0.000357 7.96
> 1609 4 2 1 control BMP2 -2.30 13.1 -20.3 0.000357 7.78
> However, the help for toptable specifies "A" as an input parameter.
> How did the "A" column appear in the output when it was not specified as an input argument?
> Thanks much,
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