What's your session info after loading aroma.affymetrix and calmate? Henrik
On Jan 4, 2013 9:59 PM, "Zheng Siyuan" <syzhen...@gmail.com> wrote: > > Hi, > I have been using Calmate to process my affy SNP6 array data. The goal is to call calibrated allele specific copy number. However, I ran into an error following the vignette http://aroma-project.org/vignettes/CalMaTe. The code is as following > > library(aroma.affymetrix) > library(calmate) > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > dataSet <- 'mydata' > chipType <- "GenomeWideSNP_6" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full") > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > #print(csR) > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose) > #print(dsList) > > Error message is > > ... > 20130104 14:42:50| Fitting...done > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of 7...done > 20130104 14:42:50| Fitting calibration model...done > Error in UseMethod("sapply") : > no applicable method for 'sapply' applied to an object of class "list" > 20130104 14:42:50| Array #1 ('0064.01') of 2...done > 20130104 14:42:50| Calibrating 2 arrays...done > 20130104 14:42:50| Calibrating data set for allelic cross talk...done > > Appears it is almost done until this small glitch. > Any comments? > > Thank you. > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/