Re: [aroma.affymetrix] calmate error (doASCRMAv2)
It is working now. Thanks.
On Sun, Jan 6, 2013 at 9:30 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Try with calmate v0.10.0, which you can install by:
>
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("calmate")
>
> Let me know if this solves it for you.
>
> /Henrik
>
> On Fri, Jan 4, 2013 at 3:32 PM, Siyuan Zheng wrote:
> > Thank you.
> >
> >
> > On Fri, Jan 4, 2013 at 5:30 PM, Henrik Bengtsson
> > wrote:
> >>
> >>
> >> On Jan 4, 2013 11:57 PM, "Zheng Siyuan" wrote:
> >> >
> >> > Hi Henrik,
> >> >
> >> > Along the path from ASCRMAv2 to CalMaTe, there comes another error.
> >> >
> >> > Code:
> >> >
> >> > dataSet <- 'mydata'
> >> > chipType <- "GenomeWideSNP_6"
> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> >> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> >> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> >> > cmt <- CalMaTeCalibration(dsList);
> >> > dsCList <- process(cmt, verbose=verbose);
> >> >
> >> > Error message:
> >> > 20130104 16:48:19|CalMaTe calibration of ASCNs...
> >> > 20130104 16:48:19| Number of arrays: 6
> >> > 20130104 16:48:19| Number of references: 6
> >> > 20130104 16:48:19| Units:
> >> > int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
> >> > 20130104 16:48:19| All parameters:
> >> > List of 2
> >> > $ references: int [1:3] 2 4 6
> >> > $ flavor: chr "v2"
> >> > 20130104 16:48:19| Skipping already processed units...
> >> > Error: 'sapply' is not an exported object from 'namespace:R.filesets'
> >>
> >> It turns out that the most recent updates of aroma. * and friends made
> >> some parts of calmate non- working. I'll fix that over the weekend and
> post
> >> a fix.
> >>
> >> Thanks for reporting.
> >>
> >> Henrik
> >>
> >> > 20130104 16:48:19| Skipping already processed units...done
> >> > 20130104 16:48:19|CalMaTe calibration of ASCNs...done
> >> >
> >> > Here is the session info:
> >> > > sessionInfo()
> >> > R version 2.15.1 (2012-06-22)
> >> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >> >
> >> > locale:
> >> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> >> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> >> > [7] LC_PAPER=C 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] preprocessCore_1.18.0 sfit_0.2.0 calmate_0.9.2
> >> > [4] MASS_7.3-22aroma.affymetrix_2.8.0 affxparser_1.28.1
> >> > [7] aroma.apd_0.2.3R.huge_0.4.1 aroma.light_1.24.0
> >> > [10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
> >> > [13] R.devices_2.1.3R.cache_0.6.5 R.filesets_1.9.0
> >> > [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
> >> >
> >> > loaded via a namespace (and not attached):
> >> > [1] digest_0.6.0 PSCBS_0.30.0
> >> >
> >> > Have you seen this before?
> >> > Thanks.
> >> >
> >> > Siyuan
> >> > MD Anderson
> >> >
> >> >
> >> >
> >> > On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
> >> >>
> >> >> you are right. Problem is solved after updating aroma.affymetrix to
> the
> >> >> latest version.
> >> >> Thank you
> >> >>
> >> >> On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
> >> >>>
> >> >>> What's your session info after loading aroma.affymetrix and calmate?
> >> >>>
> >> >>> Henrik
> >> >>>
> >> >>> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
> >> >>> >
> >> >>> > Hi,
> >> >>> > I have been using Calmate to process my affy SNP6 array data. The
> >> >>> > goal is to call calibrated allele specific copy number. However,
> I ran into
> >> >>> > an error following the vignette
> http://aroma-project.org/vignettes/CalMaTe.
> >> >>> > The code is as following
> >> >>> >
> >> >>> > library(aroma.affymetrix)
> >> >>> > library(calmate)
> >> >>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> >> >>> > dataSet <- 'mydata'
> >> >>> > chipType <- "GenomeWideSNP_6"
> >> >>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> >> >>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> >> >>> > #print(csR)
> >> >>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> >> >>> > #print(dsList)
> >> >>> >
> >> >>> > Error message is
> >> >>> >
> >> >>> > ...
> >> >>> > 20130104 14:42:50| Fitting...done
> >> >>> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
> >> >>> > 7...done
> >> >>> > 20130104 14:42:50| Fitting calibration model...done
> >> >>> > Error in UseMethod("sapply") :
> >> >>> > no applicable method for 'sapply' applied to an object of class
> >> >>> > "list"
> >> >>> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
> >> >>> > 20130104 14:42:50| Calibrating 2 arrays...done
> >> >>>
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
Try with calmate v0.10.0, which you can install by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("calmate")
Let me know if this solves it for you.
/Henrik
On Fri, Jan 4, 2013 at 3:32 PM, Siyuan Zheng wrote:
> Thank you.
>
>
> On Fri, Jan 4, 2013 at 5:30 PM, Henrik Bengtsson
> wrote:
>>
>>
>> On Jan 4, 2013 11:57 PM, "Zheng Siyuan" wrote:
>> >
>> > Hi Henrik,
>> >
>> > Along the path from ASCRMAv2 to CalMaTe, there comes another error.
>> >
>> > Code:
>> >
>> > dataSet <- 'mydata'
>> > chipType <- "GenomeWideSNP_6"
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
>> > cmt <- CalMaTeCalibration(dsList);
>> > dsCList <- process(cmt, verbose=verbose);
>> >
>> > Error message:
>> > 20130104 16:48:19|CalMaTe calibration of ASCNs...
>> > 20130104 16:48:19| Number of arrays: 6
>> > 20130104 16:48:19| Number of references: 6
>> > 20130104 16:48:19| Units:
>> > int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20130104 16:48:19| All parameters:
>> > List of 2
>> > $ references: int [1:3] 2 4 6
>> > $ flavor: chr "v2"
>> > 20130104 16:48:19| Skipping already processed units...
>> > Error: 'sapply' is not an exported object from 'namespace:R.filesets'
>>
>> It turns out that the most recent updates of aroma. * and friends made
>> some parts of calmate non- working. I'll fix that over the weekend and post
>> a fix.
>>
>> Thanks for reporting.
>>
>> Henrik
>>
>> > 20130104 16:48:19| Skipping already processed units...done
>> > 20130104 16:48:19|CalMaTe calibration of ASCNs...done
>> >
>> > Here is the session info:
>> > > sessionInfo()
>> > R version 2.15.1 (2012-06-22)
>> > Platform: x86_64-unknown-linux-gnu (64-bit)
>> >
>> > locale:
>> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> > [7] LC_PAPER=C 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] preprocessCore_1.18.0 sfit_0.2.0 calmate_0.9.2
>> > [4] MASS_7.3-22aroma.affymetrix_2.8.0 affxparser_1.28.1
>> > [7] aroma.apd_0.2.3R.huge_0.4.1 aroma.light_1.24.0
>> > [10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
>> > [13] R.devices_2.1.3R.cache_0.6.5 R.filesets_1.9.0
>> > [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
>> >
>> > loaded via a namespace (and not attached):
>> > [1] digest_0.6.0 PSCBS_0.30.0
>> >
>> > Have you seen this before?
>> > Thanks.
>> >
>> > Siyuan
>> > MD Anderson
>> >
>> >
>> >
>> > On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
>> >>
>> >> you are right. Problem is solved after updating aroma.affymetrix to the
>> >> latest version.
>> >> Thank you
>> >>
>> >> On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
>> >>>
>> >>> What's your session info after loading aroma.affymetrix and calmate?
>> >>>
>> >>> Henrik
>> >>>
>> >>> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>> >>> >
>> >>> > Hi,
>> >>> > I have been using Calmate to process my affy SNP6 array data. The
>> >>> > goal is to call calibrated allele specific copy number. However, I ran
>> >>> > into
>> >>> > an error following the vignette
>> >>> > http://aroma-project.org/vignettes/CalMaTe.
>> >>> > The code is as following
>> >>> >
>> >>> > library(aroma.affymetrix)
>> >>> > library(calmate)
>> >>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> >>> > dataSet <- 'mydata'
>> >>> > chipType <- "GenomeWideSNP_6"
>> >>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
>> >>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
>> >>> > #print(csR)
>> >>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
>> >>> > #print(dsList)
>> >>> >
>> >>> > Error message is
>> >>> >
>> >>> > ...
>> >>> > 20130104 14:42:50| Fitting...done
>> >>> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
>> >>> > 7...done
>> >>> > 20130104 14:42:50| Fitting calibration model...done
>> >>> > Error in UseMethod("sapply") :
>> >>> > no applicable method for 'sapply' applied to an object of class
>> >>> > "list"
>> >>> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
>> >>> > 20130104 14:42:50| Calibrating 2 arrays...done
>> >>> > 20130104 14:42:50| Calibrating data set for allelic cross
>> >>> > talk...done
>> >>> >
>> >>> > Appears it is almost done until this small glitch.
>> >>> > Any comments?
>> >>> >
>> >>> > Thank you.
>> >>> >
>> >>> > --
>> >>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >>> > latest version of the package, 2) to report the output of
>> >>> >
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
Thank you.
On Fri, Jan 4, 2013 at 5:30 PM, Henrik Bengtsson wrote:
>
> On Jan 4, 2013 11:57 PM, "Zheng Siyuan" wrote:
> >
> > Hi Henrik,
> >
> > Along the path from ASCRMAv2 to CalMaTe, there comes another error.
> >
> > Code:
> >
> > dataSet <- 'mydata'
> > chipType <- "GenomeWideSNP_6"
> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> > cmt <- CalMaTeCalibration(dsList);
> > dsCList <- process(cmt, verbose=verbose);
> >
> > Error message:
> > 20130104 16:48:19|CalMaTe calibration of ASCNs...
> > 20130104 16:48:19| Number of arrays: 6
> > 20130104 16:48:19| Number of references: 6
> > 20130104 16:48:19| Units:
> > int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
> > 20130104 16:48:19| All parameters:
> > List of 2
> > $ references: int [1:3] 2 4 6
> > $ flavor: chr "v2"
> > 20130104 16:48:19| Skipping already processed units...
> > Error: 'sapply' is not an exported object from 'namespace:R.filesets'
>
> It turns out that the most recent updates of aroma. * and friends made
> some parts of calmate non- working. I'll fix that over the weekend and post
> a fix.
>
> Thanks for reporting.
>
> Henrik
>
> > 20130104 16:48:19| Skipping already processed units...done
> > 20130104 16:48:19|CalMaTe calibration of ASCNs...done
> >
> > Here is the session info:
> > > sessionInfo()
> > R version 2.15.1 (2012-06-22)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=C 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] preprocessCore_1.18.0 sfit_0.2.0 calmate_0.9.2
> > [4] MASS_7.3-22aroma.affymetrix_2.8.0 affxparser_1.28.1
> > [7] aroma.apd_0.2.3R.huge_0.4.1 aroma.light_1.24.0
> > [10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
> > [13] R.devices_2.1.3R.cache_0.6.5 R.filesets_1.9.0
> > [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
> >
> > loaded via a namespace (and not attached):
> > [1] digest_0.6.0 PSCBS_0.30.0
> >
> > Have you seen this before?
> > Thanks.
> >
> > Siyuan
> > MD Anderson
> >
> >
> >
> > On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
> >>
> >> you are right. Problem is solved after updating aroma.affymetrix to the
> latest version.
> >> Thank you
> >>
> >> On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
> >>>
> >>> What's your session info after loading aroma.affymetrix and calmate?
> >>>
> >>> Henrik
> >>>
> >>> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
> >>> >
> >>> > Hi,
> >>> > I have been using Calmate to process my affy SNP6 array data. The
> goal is to call calibrated allele specific copy number. However, I ran into
> an error following the vignette http://aroma-project.org/vignettes/CalMaTe.
> The code is as following
> >>> >
> >>> > library(aroma.affymetrix)
> >>> > library(calmate)
> >>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> >>> > dataSet <- 'mydata'
> >>> > chipType <- "GenomeWideSNP_6"
> >>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> >>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> >>> > #print(csR)
> >>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> >>> > #print(dsList)
> >>> >
> >>> > Error message is
> >>> >
> >>> > ...
> >>> > 20130104 14:42:50| Fitting...done
> >>> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
> 7...done
> >>> > 20130104 14:42:50| Fitting calibration model...done
> >>> > Error in UseMethod("sapply") :
> >>> > no applicable method for 'sapply' applied to an object of class
> "list"
> >>> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
> >>> > 20130104 14:42:50| Calibrating 2 arrays...done
> >>> > 20130104 14:42:50| Calibrating data set for allelic cross
> talk...done
> >>> >
> >>> > Appears it is almost done until this small glitch.
> >>> > Any comments?
> >>> >
> >>> > Thank you.
> >>> >
> >>> > --
> >>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
> >>> >
> >>> >
> >>> > You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/
> .
> >>> > To post to this group, send email to aroma-af...@googlegroups.com
> >>> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
> > --
> > When reporting prob
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
On Jan 4, 2013 11:57 PM, "Zheng Siyuan" wrote:
>
> Hi Henrik,
>
> Along the path from ASCRMAv2 to CalMaTe, there comes another error.
>
> Code:
>
> dataSet <- 'mydata'
> chipType <- "GenomeWideSNP_6"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> cmt <- CalMaTeCalibration(dsList);
> dsCList <- process(cmt, verbose=verbose);
>
> Error message:
> 20130104 16:48:19|CalMaTe calibration of ASCNs...
> 20130104 16:48:19| Number of arrays: 6
> 20130104 16:48:19| Number of references: 6
> 20130104 16:48:19| Units:
> int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
> 20130104 16:48:19| All parameters:
> List of 2
> $ references: int [1:3] 2 4 6
> $ flavor: chr "v2"
> 20130104 16:48:19| Skipping already processed units...
> Error: 'sapply' is not an exported object from 'namespace:R.filesets'
It turns out that the most recent updates of aroma. * and friends made some
parts of calmate non- working. I'll fix that over the weekend and post a
fix.
Thanks for reporting.
Henrik
> 20130104 16:48:19| Skipping already processed units...done
> 20130104 16:48:19|CalMaTe calibration of ASCNs...done
>
> Here is the session info:
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C 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] preprocessCore_1.18.0 sfit_0.2.0 calmate_0.9.2
> [4] MASS_7.3-22aroma.affymetrix_2.8.0 affxparser_1.28.1
> [7] aroma.apd_0.2.3R.huge_0.4.1 aroma.light_1.24.0
> [10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
> [13] R.devices_2.1.3R.cache_0.6.5 R.filesets_1.9.0
> [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.0 PSCBS_0.30.0
>
> Have you seen this before?
> Thanks.
>
> Siyuan
> MD Anderson
>
>
>
> On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
>>
>> you are right. Problem is solved after updating aroma.affymetrix to the
latest version.
>> Thank you
>>
>> On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
>>>
>>> What's your session info after loading aroma.affymetrix and calmate?
>>>
>>> Henrik
>>>
>>> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>>> >
>>> > Hi,
>>> > I have been using Calmate to process my affy SNP6 array data. The
goal is to call calibrated allele specific copy number. However, I ran into
an error following the vignette http://aroma-project.org/vignettes/CalMaTe.
The code is as following
>>> >
>>> > library(aroma.affymetrix)
>>> > library(calmate)
>>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>>> > dataSet <- 'mydata'
>>> > chipType <- "GenomeWideSNP_6"
>>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
>>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
>>> > #print(csR)
>>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
>>> > #print(dsList)
>>> >
>>> > Error message is
>>> >
>>> > ...
>>> > 20130104 14:42:50| Fitting...done
>>> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
7...done
>>> > 20130104 14:42:50| Fitting calibration model...done
>>> > Error in UseMethod("sapply") :
>>> > no applicable method for 'sapply' applied to an object of class
"list"
>>> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
>>> > 20130104 14:42:50| Calibrating 2 arrays...done
>>> > 20130104 14:42:50| Calibrating data set for allelic cross talk...done
>>> >
>>> > Appears it is almost done until this small glitch.
>>> > Any comments?
>>> >
>>> > Thank you.
>>> >
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
>>> >
>>> >
>>> > You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> > To post to this group, send email to aroma-af...@googlegroups.com
>>> > To unsubscribe and other options, go to
http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
Hi Henrik,
Along the path from ASCRMAv2 to CalMaTe, there comes another error.
Code:
dataSet <- 'mydata'
chipType <- "GenomeWideSNP_6"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
cmt <- CalMaTeCalibration(dsList);
dsCList <- process(cmt, verbose=verbose);
Error message:
20130104 16:48:19|CalMaTe calibration of ASCNs...
20130104 16:48:19| Number of arrays: 6
20130104 16:48:19| Number of references: 6
20130104 16:48:19| Units:
int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ...
20130104 16:48:19| All parameters:
List of 2
$ references: int [1:3] 2 4 6
$ flavor: chr "v2"
20130104 16:48:19| Skipping already processed units...
*Error: 'sapply' is not an exported object from 'namespace:R.filesets'*
20130104 16:48:19| Skipping already processed units...done
20130104 16:48:19|CalMaTe calibration of ASCNs...done
Here is the session info:
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C 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] preprocessCore_1.18.0 sfit_0.2.0 calmate_0.9.2
[4] MASS_7.3-22aroma.affymetrix_2.8.0 affxparser_1.28.1
[7] aroma.apd_0.2.3R.huge_0.4.1 aroma.light_1.24.0
[10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
[13] R.devices_2.1.3R.cache_0.6.5 R.filesets_1.9.0
[16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] digest_0.6.0 PSCBS_0.30.0
Have you seen this before?
Thanks.
Siyuan
MD Anderson
On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
>
> you are right. Problem is solved after updating aroma.affymetrix to the
> latest version.
> Thank you
>
> On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
>>
>> What's your session info after loading aroma.affymetrix and calmate?
>>
>> Henrik
>>
>> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>> >
>> > Hi,
>> > I have been using Calmate to process my affy SNP6 array data. The goal
>> is to call calibrated allele specific copy number. However, I ran into an
>> error following the vignette http://aroma-project.org/vignettes/CalMaTe.
>> The code is as following
>> >
>> > library(aroma.affymetrix)
>> > library(calmate)
>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> > dataSet <- 'mydata'
>> > chipType <- "GenomeWideSNP_6"
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
>> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
>> > #print(csR)
>> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
>> > #print(dsList)
>> >
>> > Error message is
>> >
>> > ...
>> > 20130104 14:42:50| Fitting...done
>> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
>> 7...done
>> > 20130104 14:42:50| Fitting calibration model...done
>> > Error in UseMethod("sapply") :
>> > no applicable method for 'sapply' applied to an object of class "list"
>> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
>> > 20130104 14:42:50| Calibrating 2 arrays...done
>> > 20130104 14:42:50| Calibrating data set for allelic cross talk...done
>> >
>> > Appears it is almost done until this small glitch.
>> > Any comments?
>> >
>> > Thank you.
>> >
>> > --
>> > 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-af...@googlegroups.com
>> > To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>
--
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/
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
you are right. Problem is solved after updating aroma.affymetrix to the
latest version.
Thank you
On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
>
> What's your session info after loading aroma.affymetrix and calmate?
>
> Henrik
>
> On Jan 4, 2013 9:59 PM, "Zheng Siyuan" >
> wrote:
> >
> > Hi,
> > I have been using Calmate to process my affy SNP6 array data. The goal
> is to call calibrated allele specific copy number. However, I ran into an
> error following the vignette http://aroma-project.org/vignettes/CalMaTe.
> The code is as following
> >
> > library(aroma.affymetrix)
> > library(calmate)
> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> > dataSet <- 'mydata'
> > chipType <- "GenomeWideSNP_6"
> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> > #print(csR)
> > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> > #print(dsList)
> >
> > Error message is
> >
> > ...
> > 20130104 14:42:50| Fitting...done
> > 20130104 14:42:50| Allele probe-pair group #7 ('missing') of
> 7...done
> > 20130104 14:42:50| Fitting calibration model...done
> > Error in UseMethod("sapply") :
> > no applicable method for 'sapply' applied to an object of class "list"
> > 20130104 14:42:50|Array #1 ('0064.01') of 2...done
> > 20130104 14:42:50| Calibrating 2 arrays...done
> > 20130104 14:42:50| Calibrating data set for allelic cross talk...done
> >
> > Appears it is almost done until this small glitch.
> > Any comments?
> >
> > Thank you.
> >
> > --
> > 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-af...@googlegroups.com
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
--
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/
Re: [aroma.affymetrix] calmate error (doASCRMAv2)
What's your session info after loading aroma.affymetrix and calmate?
Henrik
On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>
> Hi,
> I have been using Calmate to process my affy SNP6 array data. The goal is
to call calibrated allele specific copy number. However, I ran into an
error following the vignette http://aroma-project.org/vignettes/CalMaTe.
The code is as following
>
> library(aroma.affymetrix)
> library(calmate)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> dataSet <- 'mydata'
> chipType <- "GenomeWideSNP_6"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full")
> csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
> #print(csR)
> dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose)
> #print(dsList)
>
> Error message is
>
> ...
> 20130104 14:42:50| Fitting...done
> 20130104 14:42:50| Allele probe-pair group #7 ('missing') of 7...done
> 20130104 14:42:50| Fitting calibration model...done
> Error in UseMethod("sapply") :
> no applicable method for 'sapply' applied to an object of class "list"
> 20130104 14:42:50|Array #1 ('0064.01') of 2...done
> 20130104 14:42:50| Calibrating 2 arrays...done
> 20130104 14:42:50| Calibrating data set for allelic cross talk...done
>
> Appears it is almost done until this small glitch.
> Any comments?
>
> Thank you.
>
> --
> 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/
--
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/
