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.
>
>
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-- 
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.


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