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
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>> >> 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.
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