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 <sshshoh1...@gmail.com> 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_0.19.3 aroma.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_2.6.0 R.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_0.6.4 DNAcopy_1.38.1 > [5] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 tools_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 <h...@biostat.ucsf.edu> >>> 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 <sshsh...@gmail.com> >>> > 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-af...@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-affymetr...@googlegroups.com. >>> >> 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 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 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.
