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 ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099

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