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'* 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/
