you are right. Problem is solved after updating aroma.affymetrix to the latest version. Thank you
On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote: > > What's your session info after loading aroma.affymetrix and calmate? > > Henrik > > On Jan 4, 2013 9:59 PM, "Zheng Siyuan" <syzh...@gmail.com <javascript:>> > 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-af...@googlegroups.com<javascript:> > > 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/