[R] Help with the zero.weights option of plotMA3by2 function in Limma package

Florian Chain florian.chain.1 at ulaval.ca
Wed Mar 29 17:25:01 CEST 2006

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,

PS: thanks to the creator of R and the packages, by the way.

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