> Date: Thu, 11 Feb 2010 17:33:15 -0700 > From: "Anthony Bosco" <abosco at="" arc.arizona.edu=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] ?is.atomic error with betr function > Message-ID: > ? ? ? ?<6V8SzW2U.1265934795.4953820.abosco at respiratory.arizona.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear list, > > > I am having trouble using the function betr (BioC package betr).. > > I am providing the required arguments (cond, timepoint, replicate) in the > correct length and class, as well as a data matrix (exprs). > > However I get the following error > > Error: is.atomic(x) is not TRUE > > This occurs even though is.atomic(exprs) = TRUE > > I also get the following warnings... > >> warnings() > Warning messages: > 1: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 2: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 3: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 4: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 5: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 6: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 7: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 8: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 9: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 10: In mean.default(newX[, i], ...) : > ?argument is not numeric or logical: returning NA > 11: In mean.default(newX[, i], ...) : > Hi Anthony, Are you able to construct a minimal example that shows the contents of the input variables and recreates the error? It would be easier to debug if I could see the actual values being used. Martin.

Hi Martin, I have figured out that the atomic error was due to having a different number of replicates at each time point. Best regards, Anthony Bosco From: Martin Aryee <aryee@jhu.edu> To: bioconductor@stat.math.ethz.ch Cc: abosco@arc.arizona.edu Sent: Sat, 13 February, 2010 4:24:39 PM Subject: Re: [BioC] is.atomic error with betr function > Date: Thu, 11 Feb 2010 17:33:15 -0700 > From: "Anthony Bosco" <abosco@arc.arizona.edu> > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] is.atomic error with betr function > Message-ID: > <6V8SzW2U.1265934795.4953820.abosco@respiratory.arizona.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear list, > > > I am having trouble using the function betr (BioC package betr).. > > I am providing the required arguments (cond, timepoint, replicate) in the > correct length and class, as well as a data matrix (exprs). > > However I get the following error > > Error: is.atomic(x) is not TRUE > > This occurs even though is.atomic(exprs) = TRUE > > I also get the following warnings... > >> warnings() > Warning messages: > 1: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 2: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 3: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 4: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 5: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 6: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 7: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 8: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 9: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 10: In mean.default(newX[, i], ...) : > argument is not numeric or logical: returning NA > 11: In mean.default(newX[, i], ...) : > Hi Anthony, Are you able to construct a minimal example that shows the contents of the input variables and recreates the error? It would be easier to debug if I could see the actual values being used. Martin. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- believed to be clean. ###################################################################### ############### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ###################################################################### ############### ###################################################################### ############### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ###################################################################### ############### [[alternative HTML version deleted]]