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 <[email protected]> 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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"aroma.affymetrix" group with website http://www.aroma-project.org/.
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