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/