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.
--
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