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
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