It is working now. Thanks.

On Sun, Jan 6, 2013 at 9:30 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:

> 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
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> http://www.aroma-project.org/.
> >> > To post to this group, send email to
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> >> > 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
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> > 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
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
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>



-- 

-----------------------------------------------------
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