On Sat, Sep 20, 2014 at 9:11 PM, jjspring OH <sshshoh1...@gmail.com> 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 <sshsh...@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-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.
