This all looks good, so it's indeed a weird error that I most likely think is due to some hiccups when the 'sfit' package was installed (which defines the cfit() function).
For troubleshooting, first try: url <- "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R"; source(url) You should get a plot similar to the one in the attached PNG. If you're R installation does not support "https" (started to be optionally supported in R 3.2.0), the you can run the above script as url <- "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenotypeCone.R"; pathname <- R.utils::downloadFile(url) source(pathname) instead. If you get the error here, we have a minimal reproducible example for your problem (without the need of Affymetrix data etc). If you get the error, try to reinstall 'sfit' - in a fresh R session - as: source("http://callr.org/install#sfit[!]";) Note the exclamation mark - it forces installation even if you already got the latest version. After this, retry the above again. Did the problem go away? /Henrik On Fri, May 29, 2015 at 12:22 PM, arshi <arshiwil...@gmail.com> wrote: > Sorry about not posting that. > >> sessionInfo() > R version 3.2.0 (2015-04-16) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 14.04.2 LTS > > 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=en_US.UTF-8 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] GLAD_2.32.0 RColorBrewer_1.1-2 R.rsp_0.20.0 > [4] DNAcopy_1.42.0 sfit_0.3.0 aroma.light_2.4.0 > [7] aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.13.0 > [10] R.filesets_2.7.1 R.utils_2.0.2 R.oo_1.19.0 > [13] affxparser_1.40.0 R.methodsS3_1.7.0 > > loaded via a namespace (and not attached): > [1] matrixStats_0.14.0 digest_0.6.8 R.huge_0.9.0 PSCBS_0.44.0 > [5] splines_3.2.0 tools_3.2.0 R.cache_0.10.0 > base64enc_0.1-2 > [9] aroma.apd_0.6.0 tcltk_3.2.0 > > > On Friday, May 29, 2015 at 3:17:18 PM UTC-4, Henrik Bengtsson wrote: >> >> First of all, what versions of packages do you have, e.g. what's the >> output sessionInfo() after doing: >> >> library("aroma.affymetrix") >> library("sfit") >> sessionInfo() >> >> >> /Henrik >> >> On Fri, May 29, 2015 at 9:51 AM, arshi <arshi...@gmail.com> wrote: >> > Hi, I am following the vignette on paired total copy number analysis. >> > >> > So far, my cdf files and the rawData directory structure looks ok. When >> > I do >> > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, >> > verbose=verbose) >> > I get the following error and I can't see a dsList object created. >> > Error in UseMethod("cfit") : >> > no applicable method for 'cfit' applied to an object of class >> > "c('matrix', >> > 'double', 'numeric')" >> > >> > I am also pasting the rest of the verbose output. The error is at the >> > bottom >> > of the output. Thanks for your help! >> > >> > CRMAv2... >> > CRMAv2/Setting up CEL set... >> > AffymetrixCelSet: >> > Name: data_aroma >> > Tags: >> > Path: rawData/data_aroma/Mapping250K_Nsp >> > Platform: Affymetrix >> > Chip type: Mapping250K_Nsp >> > Number of arrays: 4 >> > Names: RCC, RCC, RCC, RCC [4] >> > Time period: 2010-06-29 12:49:28 -- 2010-11-27 00:08:30 >> > Total file size: 250.45MB >> > RAM: 0.01MB >> > CRMAv2/Setting up CEL set...done >> > CRMAv2... >> > Arguments: >> > combineAlleles: FALSE >> > arrays: >> > chr "" >> > Data set >> > AffymetrixCelSet: >> > Name: data_aroma >> > Tags: >> > Path: rawData/data_aroma/Mapping250K_Nsp >> > Platform: Affymetrix >> > Chip type: Mapping250K_Nsp >> > Number of arrays: 4 >> > Names: RCC, RCC, RCC, RCC [4] >> > Time period: 2010-06-29 12:49:28 -- 2010-11-27 00:08:30 >> > Total file size: 250.45MB >> > RAM: 0.01MB >> > Checking whether final results are available or not... >> > Checking whether final results are available or >> > not...done >> > CRMAv2/Allelic crosstalk calibration... >> > AllelicCrosstalkCalibration: >> > Data set: data_aroma >> > Input tags: >> > User tags: * >> > Asterisk ('*') tags: ACC,-XY >> > Output tags: ACC,-XY >> > Number of files: 4 (250.45MB) >> > Platform: Affymetrix >> > Chip type: Mapping250K_Nsp >> > Algorithm parameters: {rescaleBy: chr "groups", >> > targetAvg: >> > num [1:2] 2200 2200, subsetToAvg: int [1:6409592] 1 2 3 4 5 6 7 8 9 10 >> > ..., >> > mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", >> > algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 >> > 0.01 >> > 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98} >> > Output path: >> > probeData/data_aroma,ACC,-XY/Mapping250K_Nsp >> > Is done: FALSE >> > RAM: 24.46MB >> > Calibrating data set for allelic cross talk... >> > Compressing model parameter to a short format... >> > Compressing model parameter to a short format...done >> > Calibrating 4 arrays... >> > Path: probeData/data_aroma,ACC,-XY/Mapping250K_Nsp >> > Array #1 ('RCC') of 4... >> > setsOfProbes: >> > List of 2 >> > $ snps :List of 7 >> > ..$ A/C : int [1:129194, 1:2] 5555562 640260 >> > 6430798 >> > 890622 858750 4681948 347160 5718766 2746760 2790782 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "A" "C" >> > ..$ A/G : int [1:519999, 1:2] 4969704 4677672 >> > 4787718 5185370 1363100 4109892 1558340 1352256 1332280 4969616 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "A" "G" >> > ..$ A/T : int [1:107590, 1:2] 1028670 3832004 >> > 5665036 1832744 4167500 4571986 4938090 747094 2207654 5855716 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "A" "T" >> > ..$ C/G : int [1:156840, 1:2] 4747206 3909704 >> > 1725666 600232 416088 1138554 6393394 6389120 555046 2960654 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "C" "G" >> > ..$ C/T : int [1:572339, 1:2] 3789122 5491344 >> > 768382 >> > 4974648 387402 2086744 1183506 5290380 6464728 6121838 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "C" "T" >> > ..$ G/T : int [1:124838, 1:2] 2968724 1545656 >> > 2540860 5758784 3927738 3915584 4695222 2062772 6258084 4709566 ... >> > .. ..- attr(*, "dimnames")=List of 2 >> > .. .. ..$ : NULL >> > .. .. ..$ : chr [1:2] "G" "T" >> > ..$ missing: int [1:700, 1:2] 3365154 3362594 >> > 3360034 >> > 3357474 3354914 3352354 3349794 3329314 3326754 3324194 ... >> > $ nonSNPs: NULL >> > - attr(*, "version")= num 4 >> > Reading all probe intensities... >> > Reading all probe intensities...done >> > Fitting calibration model... >> > Allele probe-pair group #1 ('A/C') of 7... >> > Fitting... >> > Model/algorithm flavor: sfit >> > Model parameters: >> > List of 3 >> > $ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 >> > 0.0025 >> > 0.001 0.0001 >> > $ q : num 2 >> > $ Q : num 98 >> > Number of data points: 129194 >> > Error in UseMethod("cfit") : >> > no applicable method for 'cfit' applied to an object of class >> > "c('matrix', >> > 'double', 'numeric')" >> > Fitting...done >> > Allele probe-pair group #1 ('A/C') of 7...done >> > Fitting calibration model...done >> > Array #1 ('RCC') of 4...done >> > Calibrating 4 arrays...done >> > Calibrating data set for allelic cross talk...done >> > >> > -- >> > -- >> > 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/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to aroma-affymetr...@googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
