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 <javascript:>>
> 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.
> >
> >
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--
--
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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