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 <arshiwil...@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
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>>> > "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/
>>> >
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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.
>>
>>
>> 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
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>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to aroma-affymetrix+unsubscr...@googlegroups.com.
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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.
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/
---
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