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-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.