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