On Jan 4, 2013 11:57 PM, "Zheng Siyuan" <syzhen...@gmail.com> wrote:
>
> Hi Henrik,
>
> Along the path from ASCRMAv2 to CalMaTe, there comes another error.
>
> Code:
>
> dataSet <- 'mydata'
> chipType <- "GenomeWideSNP_6"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> cmt <- CalMaTeCalibration(dsList);
> dsCList <- process(cmt, verbose=verbose);
>
> Error message:
> 20130104 16:48:19|CalMaTe calibration of ASCNs...
> 20130104 16:48:19| Number of arrays: 6
> 20130104 16:48:19| Number of references: 6
> 20130104 16:48:19| Units:
>   int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
> 20130104 16:48:19| All parameters:
>  List of 2
>   $ references: int [1:3] 2 4 6
>   $ flavor    : chr "v2"
> 20130104 16:48:19| Skipping already processed units...
> Error: 'sapply' is not an exported object from 'namespace:R.filesets'

It turns out that the most recent updates of aroma. * and friends made some
parts of calmate non- working. I'll fix that over the weekend and post a
fix.

Thanks for reporting.

Henrik

> 20130104 16:48:19| Skipping already processed units...done
> 20130104 16:48:19|CalMaTe calibration of ASCNs...done
>
> Here is the session info:
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] preprocessCore_1.18.0  sfit_0.2.0             calmate_0.9.2
>  [4] MASS_7.3-22            aroma.affymetrix_2.8.0 affxparser_1.28.1
>  [7] aroma.apd_0.2.3        R.huge_0.4.1           aroma.light_1.24.0
> [10] aroma.core_2.8.0       matrixStats_0.6.2      R.rsp_0.8.2
> [13] R.devices_2.1.3        R.cache_0.6.5          R.filesets_1.9.0
> [16] R.utils_1.19.3         R.oo_1.11.4            R.methodsS3_1.4.2
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.0 PSCBS_0.30.0
>
> Have you seen this before?
> Thanks.
>
> Siyuan
> MD Anderson
>
>
>
> On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
>>
>> 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> 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
>>> > 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/

-- 
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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