Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-21 Thread Henrik Bengtsson 
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_0.19.3aroma.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,

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-20 Thread jjspring OH 


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 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

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-20 Thread Henrik Bengtsson 
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_0.19.3aroma.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 h...@biostat.ucsf.edu
 wrote:
  Sorry, it took me a while to spot the actual problem;
 
  display(ae)
  The file