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
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