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 > >> > 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/ > -- ----------------------------------------------------- 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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