Hi Henrik,
Can you help why I getting this error at copy number segmentation step ?
ce <- ChromosomeExplorer(cbs, zooms=2^(0:5))
process(ce, array=1:2, chromosomes=c(1,2,7,22), verbose=verbose)
Error: Failed to located UGP files for one of the chip types
(GenomeWideSNP_6.Full).
By checking the information of ugp file, seems like the file is seen ok.
> ugp <- UgpGenomeInformation$byChipType("GenomeWideSNP_6.Full")
> print(ugp)
UgpGenomeInformation:
Name: GenomeWideSNP_6.Full
Tags: na31,hg19,HB20110328
Full name: GenomeWideSNP_6.Full,na31,hg19,HB20110328
Pathname:
annotationData/chipTypes/GenomeWideSNP_6.Full/GenomeWideSNP_6.Full,na31,hg19,HB20110328.ugp
File size: 8.97 MB (9407867 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Thanks in advance
Uma
On Sat, Mar 23, 2013 at 5:52 PM, Uma Shankavaram
<uma.shankava...@gmail.com>wrote:
> Sorry, I guess I overlooked it. Many thanks for the help.
>
> Uma
>
>
> On Sat, Mar 23, 2013 at 5:45 PM, Henrik Bengtsson <
> henrik.bengts...@aroma-project.org> wrote:
>
>> On Sat, Mar 23, 2013 at 2:41 PM, Uma Shankavaram
>> <uma.shankava...@gmail.com> wrote:
>> > Yes, I found it at the aroma.affymetrix.org site under labs.
>> >
>> >
>> https://docs.google.com/document/d/1P8zyjvzpKvW1Zquys3DHCXCkzaENqILrOz99uTWxppk/edit
>>
>> Thanks. Though, at bit before that it says/said:
>>
>> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>>
>> I've changed 'log' to 'verbose', because that will always work.
>>
>> /H
>>
>> >
>> > Thx
>> >
>> > Uma
>> >
>> >
>> > On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson
>> > <henrik.bengts...@aroma-project.org> wrote:
>> >>
>> >> On Sat, Mar 23, 2013 at 2:29 PM, Uma Shankavaram
>> >> <uma.shankava...@gmail.com> wrote:
>> >> > Dear Henrik,
>> >> >
>> >> > Thanks for the prompt fix. I have re-installed the library from the
>> >> > source("http://aroma-project.org/hbLite.R";)
>> >> > hbInstall("aroma.core")
>> >> >
>> >> > Yes, it is working now, but there is still a small glitch.
>> >> > It is failing if I pass the verbose argument.
>> >> >
>> >> > e.g.
>> >> > process(ae, verbose = log)
>> >> >
>> >> > gives an error:
>> >> > at #01. process(ae, verbose = log)
>> >> > - process() is in environment 'aroma.core'
>> >> >
>> >> > Error: Argument 'verbose' is not a vector: function
>> >>
>> >> So, here 'log' probably equals base::log. Use verbose=TRUE (default)
>> >> or a (negative) value, e.g. verbose=-10 (verbose=-20 shows more).
>> >>
>> >> Is there an (online?) example showing "process(ae, verbose = log)"
>> >> that needs to be corrected?
>> >>
>> >> /Henrik
>> >>
>> >>
>> >> >>>>>>>>>>>>>>>>>>>>>>
>> >> > However, without verbose argument, gets the result.
>> >> > process(ae)
>> >> > Color maps: sqrt,yellow
>> >> > Chip type: GenomeWideSNP_6.Full
>> >> > Samples: GSM557940, GSM557941, GSM557942
>> >> > Aliases: GSM557940, GSM557941, GSM557942
>> >> > Color maps: sqrt,yellow
>> >> > Chip type: GenomeWideSNP_6.Full
>> >> > Samples: GSM557940, GSM557941, GSM557942
>> >> > Aliases: GSM557940, GSM557941, GSM557942
>> >> > [1] FALSE
>> >> >
>> >> >
>> >> > Uma
>> >> >
>> >> > On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson
>> >> > <henrik.bengts...@aroma-project.org> wrote:
>> >> >>
>> >> >> I've fixed this. Running.
>> >> >>
>> >> >> source("http://aroma-project.org/hbLite.R";)
>> >> >> hbInstall("aroma.core")
>> >> >>
>> >> >> should fix this (you'll get aroma.core v2.8.3). Please let me know
>> if
>> >> >> this solved your problem.
>> >> >>
>> >> >> /Henrik
>> >> >>
>> >> >> PS. The problem appears when installing the R-forge binary of
>> >> >> aroma.core (which in turn is due to temporary updates in R.rsp,
>> which
>> >> >> [is too much to explain]). I *think* this would only hit people who
>> >> >> have R-forge setup in their getOption("repos") or install directly
>> >> >> from R-forge, so most people would not be affected by this. I've
>> >> >> updated hbInstall() to never install from R-forge. FYI, don't
>> install
>> >> >> from R-forge, because that contains my non-official
>> under-construction
>> >> >> and non-tested updates.
>> >> >>
>> >> >>
>> >> >> On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
>> >> >> <henrik.bengts...@gmail.com> wrote:
>> >> >> > I can reproduce this - very odd. I'll investigate a fix it. In
>> the
>> >> >> > meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g.
>> >> >> >
>> >> >> > install.packages("aroma.core", repos="@CRAN@")
>> >> >> > install.packages("aroma.affymetrix", repos="@CRAN@")
>> >> >> >
>> >> >> > (Add repos="@CRAN@" to make sure not to install from other
>> >> >> > repositories.)
>> >> >> >
>> >> >> > Thanks for the report,
>> >> >> >
>> >> >> > Henrik
>> >> >> >
>> >> >> > On Sat, Mar 23, 2013 at 10:16 AM, Uma Shankavaram
>> >> >> > <uma.shankava...@gmail.com> wrote:
>> >> >> >> Hello,
>> >> >> >>
>> >> >> >> I am using aroma.affymetrix_2.8.2 package using Windows version
>> of R
>> >> >> >> to
>> >> >> >> process 4 SNP6.0 cel files.
>> >> >> >> I am getting an error when trying to use this function.
>> >> >> >>
>> >> >> >> e.g.
>> >> >> >> ae <- ArrayExplorer(csR)
>> >> >> >> setColorMaps(ae, "sqrt,yellow")
>> >> >> >> process(ae, verbose = log)
>> >> >> >> ...
>> >> >> >> Error: could not find function "process"
>> >> >> >>
>> >> >> >> Can anyone know why there is a problem?
>> >> >> >>
>> >> >> >> My R session info is:
>> >> >> >>> sessionInfo()
>> >> >> >> R version 2.15.1 (2012-06-22)
>> >> >> >> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> >> >> >>
>> >> >> >> locale:
>> >> >> >> [1] LC_COLLATE=English_United States.1252
>> LC_CTYPE=English_United
>> >> >> >> States.1252 LC_MONETARY=English_United States.1252
>> >> >> >> [4] LC_NUMERIC=C LC_TIME=English_United
>> >> >> >> States.1252
>> >> >> >>
>> >> >> >> attached base packages:
>> >> >> >> [1] stats graphics grDevices utils datasets methods
>> base
>> >> >> >>
>> >> >> >> other attached packages:
>> >> >> >> [1] aroma.affymetrix_2.8.2 affxparser_1.30.2
>> aroma.apd_0.2.3
>> >> >> >> R.huge_0.4.2 aroma.light_1.24.0
>> >> >> >> [6] aroma.core_2.8.2 matrixStats_0.6.2 R.rsp_0.8.2
>> >> >> >> R.devices_2.1.3 R.cache_0.6.8
>> >> >> >> [11] R.filesets_2.0.1 R.utils_1.19.5 R.oo_1.13.0
>> >> >> >> R.methodsS3_1.4.2
>> >> >> >>
>> >> >> >> loaded via a namespace (and not attached):
>> >> >> >> [1] digest_0.6.3 PSCBS_0.30.0 tools_2.15.1
>> >> >> >>
>> >> >> >>
>> >> >> >> Thanks
>> >> >> >>
>> >> >> >> Uma
>> >> >> >>
>> >> >> >> --
>> >> >> >> --
>> >> >> >> 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
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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.
>> >> >>
>> >> >>
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>> .
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>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Uma
>> >> >
>> >> > --
>> >> > --
>> >> > 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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>> >> > To post to this group, send email to
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>> >> > To unsubscribe and other options, go to
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>> >> >
>> >> > ---
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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
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>> >>
>> >
>> >
>> >
>> > --
>> > Uma
>> >
>> > --
>> > --
>> > 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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>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go to
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>> >
>> > ---
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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
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>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to
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>>
>> ---
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>>
>>
>
>
> --
> Uma
>
--
Uma
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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traceback(), and 3) to post a complete code example.
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