[BioC] limma toptable output

[James Wettenhall]

Dick,

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 
"names(fit)".

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.

Regards,
James

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,
> Dick