[BioC] Using MAANOVA functions

[James W. MacDonald]

Heather Maughan wrote:
> Dear Bioconductor-users:
> 
> I am using the package MAANOVA to analyze microarray data and have
> encountered problems when trying to plot data.  I have tried emailing a
> MAANOVA discussion group, as well as the author of the package, and have not
> yet received a response so I am hoping that someone on this listserv can be
> of assistance.  
> 
> There are several functions in MAANOVA (riplot, resiplot) which call the
> "plot" function.  For some unknown reason, when I use these functions, it
> appears that "xlim" has not been specified and I get an error (see below).
> However, when reading the code for each function, a command for how to
> calculate "xlim" has been specified but for some reason it does not get
> done.  Does anyone have experience using MAANOVA commands and is willing to
> help?
> 
> Here is an example of the error I get.  It is identical also for the
> "resiplot" command:
> 
> 
>>riplot(spore)
> 
> Error in plot.window(xlim, ylim, log, asp, ...) :
>     need finite 'xlim' values

Looks like the calculation of xlim results in either an Inf or -Inf. 
Your best bet is to run riplot() under the debugger and see what is 
being passed to plot().

debug(riplot)
riplot(spore)

You will be able to step through the function and see what you get for 
max(I) and min(I), which may help figure out what is happening.

HTH,

Jim


> 
> Many thanks,
> Heather
> --
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623