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/

Reply via email to