I was able to get the plot. But I reinstalled sfit anyways and it works
now! Thanks so much Henrik.
I get a lot of these warnings after running - any advice ?
Argument 'centers' for matrixStats::rowMads() has been renamed to
'center'. Please update code accordingly.
I also get this warning at cbs stage.
In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, data.type =
"logratio", :
array has repeated maploc positions
Thanks so much!
Arshi
On Friday, May 29, 2015 at 7:35:13 PM UTC-4, Henrik Bengtsson wrote:
>
> 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 <[email protected]
> <javascript:>> 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 <[email protected]
> <javascript:>> 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 <[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.
> >>> >
> >>> >
> >>> > 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 [email protected]
> >>> > 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 [email protected].
> >>> > For more options, visit https://groups.google.com/d/optout.
> >>
> >> --
> >> --
> >> 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 [email protected]
> <javascript:>
> >> 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 [email protected] <javascript:>.
> >> For more options, visit https://groups.google.com/d/optout.
>
--
--
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 [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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