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.

Dear Florian, Thanks for pointing this out. It is a bug and not your mistake. I'll fix it for limma 2.7.2. Best wishes Gordon At 08:00 PM 3/05/2006, bioconductor-request at stat.math.ethz.ch wrote: >Date: Tue, 02 May 2006 13:53:57 -0400 >From: Florian Chain <florian.chain.1 at="" ulaval.ca=""> >Subject: [BioC] Help with the zero.weights option of plotMA3by2 > function in Limma package >To: bioconductor at stat.math.ethz.ch > >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.