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 Many thanks, Heather --

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

Hi Heather, Are you trying the riplot function on one-color data? It only works for two-color as far as I know from previous versions. I have not tried the new version yet. Otherwise, you may have some missing or strange entries in some cells. Good luck, Xiangqin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Heather Maughan Sent: Tuesday, December 20, 2005 5:19 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Using MAANOVA functions 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 Many thanks, Heather -- _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor