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. 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