edgeR package: plotMDS warnings

[capricy]

When I tried to specify the method using "logFC", a series of warning messaged came up:

plotMDS(y,col=color,method="logFC")
Warning messages:
1: In plot.window(...) : "method" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "method" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
"method" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
"method" is not a graphical parameter
5: In box(...) : "method" is not a graphical parameter
6: In title(...) : "method" is not a graphical parameter

what is the default method? How should I fix this issue?

Thanks a lot for any input

[jaavedm]

I don't see a method argument to the plotMDS function in help page. plotMDS is a wrapper function to R's plot function, so any argument plotMDS does not understand, it automatically sends it to plot. Plot in this case does not know what the method argument is either.

How did you decide to call plotMDS in this way. Are you following an example in the documentation of edgeR?

[capricy]

I saw it in reference manual page 76...

[jaavedm]

Ah yes. That is plotMDS.DGEList on page 76 and not plotMDS.

[capricy]

Are they different in terms of command line?