Try with calmate v0.10.0, which you can install by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("calmate")
Let me know if this solves it for you.
/Henrik
On Fri, Jan 4, 2013 at 3:32 PM, Siyuan Zheng <syzhen...@gmail.com> wrote:
> Thank you.
>
>
> On Fri, Jan 4, 2013 at 5:30 PM, Henrik Bengtsson <h...@biostat.ucsf.edu>
> wrote:
>>
>>
>> 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.
>>
>>
>> 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/
>
>
>
>
> --
>
> -----------------------------------------------------
> Life is Beautiful!
>
> --
> 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.
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/
