Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
On Sat, Sep 20, 2014 at 9:11 PM, jjspring OH wrote: > > > Thanks! Yes, it seems it is due to old version for manual example, > > > Everything is done when i follow the URL for now and getting display(ae) > result (attached file) > BTW just checking out for one warning message from plm fitting before > getting into alternative splicing part, > is it ok to ignore the message ? what exactly does it mean? > > > fit(plmTr, verbose=verbose) > > Warning message: > In fitfcn(y, ...) : > Ignoring a unit group when fitting probe-level model, because it has a > ridiculously large number of data points: 6515x8 > 5000x1 See 'models/RmaPlm/skipThreshold' on http://aroma-project.org/settings /Henrik >> > > > > > Thanks again, > Best Sunghee > > > > > > > 2014년 9월 21일 일요일 오전 1시 46분 6초 UTC+9, Henrik Bengtsson 님의 말: >> >> How are you setting up the ArrayExplorer? It looks like you're >> missing to set the color maps. Are you following a particular example >> (URL?) that could be wrong. Have a look at >> >> http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis >> >> for an example. >> >> /Henrik >> >> On Sat, Sep 20, 2014 at 4:03 AM, jjspring OH wrote: >> > >> > >> > And also, >> > >> > For process(ae) >> > >> > getting warning messages(pls see below) it seems to be related with next >> > command lines >> > it does not matter? could you please take a closer look at these as >> > well? >> > >> > curent sessionInfo is >> > >> > R version 3.1.1 (2014-07-10) >> > Platform: x86_64-apple-darwin10.8.0 (64-bit) >> > >> > locale: >> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 >> > [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 >> > [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 >> > [10] affxparser_1.36.0 R.methodsS3_1.6.1 >> > >> > loaded via a namespace (and not attached): >> > [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 >> > [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 >> >> >> > >> > >> > >> > >> > >> > >> > >> >> process(ae) >> > Loading required package: R.rsp >> > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. >> > >> > Attaching package: ‘R.rsp’ >> > >> > The following object is masked from ‘package:aroma.affymetrix’: >> > >> > getParameter >> > >> > The following objects are masked from ‘package:aroma.core’: >> > >> > getParameters, process, write >> > >> > The following objects are masked from ‘package:R.filesets’: >> > >> > getAttribute, getAttributes, getFile, getFileSize, getHeader, >> > nbrOfLines, setAttribute, setAttributes >> > >> > The following objects are masked from ‘package:R.utils’: >> > >> > parse, parse.default >> > >> > The following objects are masked from ‘package:base’: >> > >> > flush, parse, stop, write >> > >> > The following object is masked _by_ package:aroma.affymetrix: >> > >> > writeCdf >> > >> > The following object is masked _by_ package:R.utils: >> > >> > findFiles >> > >> > 20140920 19:48:32|Color maps: >> > 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 >> > 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ >> > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS >> > _ >> > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 5_(RaGene-1_0-st-v1),residuals >> > 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ >> > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ >> > 8_(RaGene-1_0-st-v1), >> > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ >> > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) >> > 20140920 19:48:47|Color maps: >> > 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 >> > 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ >> > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS >> > _ >> > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS >> > _ >> > 5_(RaGene-1_0-st-v1),residuals >> > 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ >> > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ >> > 8_(RaGene-1_0-st-v1), >> > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ >> > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) >> > [1] FALSE >> > Warning messages: >> > 1: In fcn(...) : Packages reordered in search path: package:affxparser >> > 2: In parseRepos(sets = repos, where = where, fallback = fallback, : >> > Had to fall back to a set of predefined repositories (please make sure >> > to >> > set your package repositories p
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
How are you setting up the ArrayExplorer? It looks like you're missing to set the color maps. Are you following a particular example (URL?) that could be wrong. Have a look at http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis for an example. /Henrik On Sat, Sep 20, 2014 at 4:03 AM, jjspring OH wrote: > > > And also, > > For process(ae) > > getting warning messages(pls see below) it seems to be related with next > command lines > it does not matter? could you please take a closer look at these as well? > > curent sessionInfo is > > R version 3.1.1 (2014-07-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 > [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 > [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 > [10] affxparser_1.36.0 R.methodsS3_1.6.1 > > loaded via a namespace (and not attached): > [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 > [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 >> > > > > > > > >> process(ae) > Loading required package: R.rsp > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. > > Attaching package: ‘R.rsp’ > > The following object is masked from ‘package:aroma.affymetrix’: > > getParameter > > The following objects are masked from ‘package:aroma.core’: > > getParameters, process, write > > The following objects are masked from ‘package:R.filesets’: > > getAttribute, getAttributes, getFile, getFileSize, getHeader, > nbrOfLines, setAttribute, setAttributes > > The following objects are masked from ‘package:R.utils’: > > parse, parse.default > > The following objects are masked from ‘package:base’: > > flush, parse, stop, write > > The following object is masked _by_ package:aroma.affymetrix: > > writeCdf > > The following object is masked _by_ package:R.utils: > > findFiles > > 20140920 19:48:32|Color maps: > 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 > 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > 20140920 19:48:47|Color maps: > 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 > 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > [1] FALSE > Warning messages: > 1: In fcn(...) : Packages reordered in search path: package:affxparser > 2: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = > aliases, : > No color maps specified. Nothing to do. > 5: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > > > > Many Thanks! > > Sunghee > > > 2014년 9월 20일 토요일 오후 7시 58분 39초 UTC+9, jjspring OH 님의 말: >> >> >> >> >> Thanks Henrik, >> >> Yes, There is no error message on the command line display(ae) but when i >> open up the file under the directory (/results ... .html) with safari >> Its not working and the result is not shown, >> I have attached screen image file to show up, Could you please take a look >> at and doublecheck? >> >> >> Thanks a lot >> >> Sunghee >> >> >> >> >> >> >> >> 2014년 9월 20일 토요일 오전 8시 3분 52초 UTC+9, Henrik Bengtsson 님의 말: >>> >>> On Fri, Sep 19, 2014 a
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
And also, For process(ae) getting warning messages(pls see below) it seems to be related with next command lines it does not matter? could you please take a closer look at these as well? curent sessionInfo is R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 [10] affxparser_1.36.0 R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 > > process(ae) Loading required package: R.rsp R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. Attaching package: ‘R.rsp’ The following object is masked from ‘package:aroma.affymetrix’: getParameter The following objects are masked from ‘package:aroma.core’: getParameters, process, write The following objects are masked from ‘package:R.filesets’: getAttribute, getAttributes, getFile, getFileSize, getHeader, nbrOfLines, setAttribute, setAttributes The following objects are masked from ‘package:R.utils’: parse, parse.default The following objects are masked from ‘package:base’: flush, parse, stop, write The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked _by_ package:R.utils: findFiles 20140920 19:48:32|Color maps: 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) 20140920 19:48:47|Color maps: 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) [1] FALSE Warning messages: 1: In fcn(...) : Packages reordered in search path: package:affxparser 2: In parseRepos(sets = repos, where = where, fallback = fallback, : Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’ 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = aliases, : No color maps specified. Nothing to do. 5: In parseRepos(sets = repos, where = where, fallback = fallback, : Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’ 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' Many Thanks! Sunghee 2014년 9월 20일 토요일 오후 7시 58분 39초 UTC+9, jjspring OH 님의 말: > > > > > Thanks Henrik, > > Yes, There is no error message on the command line display(ae) but when i > open up the file under the directory (/results ... .html) with safari > Its not working and the result is not shown, > I have attached screen image file to show up, Could you please take a look > at and doublecheck? > > > Thanks a lot > > Sunghee > > > > > > > > 2014년 9월 20일 토요일 오전 8시 3분 52초 UTC+9, Henrik Bengtsson 님의 말: >> >> On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson >> wrote: >> > Sorry, it took me a while to spot the actual problem; >> > >> >> display(ae) >> >> The file >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> does not exist. >> > >> > (I'm surprised there is no "error" or similar generated, but it could >> > be because that message is from an external software). >> > >> > You can always open the HTML report manually just like any other HTML >> > file. You'
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson wrote:
> Sorry, it took me a while to spot the actual problem;
>
>> display(ae)
>> The file
>> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html
>> does not exist.
>
> (I'm surprised there is no "error" or similar generated, but it could
> be because that message is from an external software).
>
> You can always open the HTML report manually just like any other HTML
> file. You'll find it at reports\tissues/RBC,QN,RMA/ArrayExplorer.html
> under your working directory.
>
> I'll investigate and fix this.
It was a bug in aroma.core making display() only opening Explorer HTML
pages on Windows. I've fixed this in aroma.core 2.12.8 and verified
that it works on OSX. Update to via:
source("http://callr.org/install#aroma.affymetrix";)
Thanks for reporting
Henrik
>
> /Henrik
>
>
>
> On Wed, Sep 17, 2014 at 5:50 PM, jjspring OH wrote:
>>
>> Hi,
>>
>>
>> I am getting errors when i run aroma.affymetrix package for dynamic reports,
>> it looks like for low level analysis, everything works well for now,
>> Could you please take a closer look at and let me know what the problem is?
>> I am running under the current directory(/foo/arom-anal/)
>>
>>
>>> process(ae)
>> Loading required package: R.rsp
>> R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help.
>>
>> Attaching package: ‘R.rsp’
>>
>> The following object is masked from ‘package:aroma.affymetrix’:
>>
>> getParameter
>>
>> The following objects are masked from ‘package:aroma.core’:
>>
>> getParameters, process, write
>>
>> The following objects are masked from ‘package:R.filesets’:
>>
>> getAttribute, getAttributes, getFile, getFileSize, getHeader,
>> nbrOfLines, setAttribute, setAttributes
>>
>> The following objects are masked from ‘package:R.utils’:
>>
>> parse, parse.default
>>
>> The following objects are masked from ‘package:base’:
>>
>> flush, parse, stop, write
>>
>> The following object is masked _by_ package:aroma.affymetrix:
>>
>> writeCdf
>>
>> The following object is masked _by_ package:R.utils:
>>
>> findFiles
>>
>> 20140918 09:43:05|Color maps:
>> 20140918 09:43:05|Chip type: RaGene-1_0-st-v1,r3
>> 20140918 09:43:12|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _
>> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _
>> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _
>> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _
>> 5_(RaGene-1_0-st-v1),residuals
>> 20140918 09:43:12|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _
>> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1),
>> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _
>> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1)
>> 20140918 09:43:20|Color maps:
>> 20140918 09:43:20|Chip type: RaGene-1_0-st-v1,r3
>> 20140918 09:43:27|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _
>> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _
>> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _
>> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _
>> 5_(RaGene-1_0-st-v1),residuals
>> 20140918 09:43:27|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _
>> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1),
>> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _
>> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1)
>> [1] FALSE
>> Warning messages:
>> 1: In fcn(...) : Packages reordered in search path: package:affxparser
>> 2: In parseRepos(sets = repos, where = where, fallback = fallback, :
>> Had to fall back to a set of predefined repositories (please make sure to
>> set your package repositories properly, cf. ?setRepositories): CRAN:
>> ‘@CRAN@’ -> ‘http://cran.r-project.org’
>> 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>> 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases =
>> aliases, :
>> No color maps specified. Nothing to do.
>> 5: In parseRepos(sets = repos, where = where, fallback = fallback, :
>> Had to fall back to a set of predefined repositories (please make sure to
>> set your package repositories properly, cf. ?setRepositories): CRAN:
>> ‘@CRAN@’ -> ‘http://cran.r-project.org’
>> 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>>> display(ae)
>>> The file
>>> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html
>>> does not exist.
>>
>>
>> Thanks a lot in advance,
>>
>> Sunghee
>>
>> --
>> --
>> 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
Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
Sorry, it took me a while to spot the actual problem; > display(ae) > The file > /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html > does not exist. (I'm surprised there is no "error" or similar generated, but it could be because that message is from an external software). You can always open the HTML report manually just like any other HTML file. You'll find it at reports\tissues/RBC,QN,RMA/ArrayExplorer.html under your working directory. I'll investigate and fix this. /Henrik On Wed, Sep 17, 2014 at 5:50 PM, jjspring OH wrote: > > Hi, > > > I am getting errors when i run aroma.affymetrix package for dynamic reports, > it looks like for low level analysis, everything works well for now, > Could you please take a closer look at and let me know what the problem is? > I am running under the current directory(/foo/arom-anal/) > > >> process(ae) > Loading required package: R.rsp > R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. > > Attaching package: ‘R.rsp’ > > The following object is masked from ‘package:aroma.affymetrix’: > > getParameter > > The following objects are masked from ‘package:aroma.core’: > > getParameters, process, write > > The following objects are masked from ‘package:R.filesets’: > > getAttribute, getAttributes, getFile, getFileSize, getHeader, > nbrOfLines, setAttribute, setAttributes > > The following objects are masked from ‘package:R.utils’: > > parse, parse.default > > The following objects are masked from ‘package:base’: > > flush, parse, stop, write > > The following object is masked _by_ package:aroma.affymetrix: > > writeCdf > > The following object is masked _by_ package:R.utils: > > findFiles > > 20140918 09:43:05|Color maps: > 20140918 09:43:05|Chip type: RaGene-1_0-st-v1,r3 > 20140918 09:43:12|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140918 09:43:12|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > 20140918 09:43:20|Color maps: > 20140918 09:43:20|Chip type: RaGene-1_0-st-v1,r3 > 20140918 09:43:27|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ > 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ > 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ > 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ > 5_(RaGene-1_0-st-v1),residuals > 20140918 09:43:27|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ > 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), > NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ > 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) > [1] FALSE > Warning messages: > 1: In fcn(...) : Packages reordered in search path: package:affxparser > 2: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = > aliases, : > No color maps specified. Nothing to do. > 5: In parseRepos(sets = repos, where = where, fallback = fallback, : > Had to fall back to a set of predefined repositories (please make sure to > set your package repositories properly, cf. ?setRepositories): CRAN: > ‘@CRAN@’ -> ‘http://cran.r-project.org’ > 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' >> display(ae) >> The file >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> does not exist. > > > Thanks a lot in advance, > > Sunghee > > -- > -- > 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. -- -- When re
