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/