On Mon, Jun 1, 2015 at 9:17 AM, Arshi Arora <arshiaur...@gmail.com> wrote: > I was able to get the plot. But I reinstalled sfit anyways and it works now! > Thanks so much Henrik.
Great to hear. > I get a lot of these warnings after running - any advice ? > > Argument 'centers' for matrixStats::rowMads() has been renamed to 'center'. > Please update code accordingly. This is a harmless _warning_ that you can happily ignore. (I actually fixed this only a few minutes ago so you won't see it in future versions, cf. https://goo.gl/PMLv0a - but it will take a while before you see the update on CRAN). > > I also get this warning at cbs stage. > In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, data.type = > "logratio", : > array has repeated maploc positions That is also a harmless warnings created by the DNAcopy implementation of CBS - it happens when two CN probes on the array happens to have the exact same genomic location. This is a warning I cannot do anything about, but again, it's harmless. Henrik > > Thanks so much! > Arshi > > On Friday, May 29, 2015 at 7:35:13 PM UTC-4, Henrik Bengtsson wrote: >> >> BTW, >> >> the output of >> >> packageDescription("sfit") >> >> is also useful for troubleshooting - it will particularly tell you >> when and for what version of R it was build and installed. >> >> /Henrik >> >> On Fri, May 29, 2015 at 4:33 PM, Henrik Bengtsson <h...@aroma-project.org> >> wrote: >> > 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 <arshi...@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-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. 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