Dear all, trying to get some insights in a data set resulting from a microarray experiment, I used the Limma package and its graphical function plotMA and plotMA3by2. I am wondering if there might be a problem with the zero.weights option. Here are the command lines I have tried, and their results > plotMA(RGflag2[,1], zero.weights=TRUE) I got a graphical display, with all data plotted for the first array of my data set named RGflag2. RGflag2 includes weights (2 possible values: 0 and 1).
> plotMA(RGflag2[,1], zero.weights=FALSE) When I use this one, I get a plot but some data are missing ( not displayed), which is correct, given the option zero.weights=FALSE However, when I tried to use plotMA3by2 > plotMA3by2(RGflag2, prefix="zero weights included", zero.weights=TRUE) > plotMA3by2(RGflag2, prefix="zero weights excluded", zero.weights=FALSE) the images I obtain are identical and correspond to plots without data having a 0 as weight value, whatever the setting (TRUE or FALSE). In other words, individually the zero.weights option gives the expected results, but when dealing with a batch of plots with the plotMA3by2 it is like it stays by default on the zero.weights=FALSE. Could anyone know if I am doing something wrong or misunderstanding the function zero.weights in the plotMA3by2 ? Thank you, Florian PS: thanks to the creator of R and the packages, by the way. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
