[aroma.affymetrix] transcript and exon level analysis for detection of alternative splicings

2014-09-21 Thread jjspring OH 


Hi,


I would like to compare the results from plmTr and plmEx, estimation of 
overall expression for transcripts and exon-by-exon estimation,
but when i tried to run ExonRmaPlm with mergeGroups = T and F, 
respectively, i am getting the identical results for following objects 
including FIRMA scores based on 29170 rows by samples,
 


plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)

print(plmTr)



plmEx - ExonRmaPlm(csN, mergeGroups=FALSE)

print(plmEx)

...



firma - FirmaModel(plmEx)

fit(firma, verbose=verbose)

fs - getFirmaScores(firma)

asData - extractDataFrame(fs, addNames=TRUE)


 fs - getFirmaScores(firma)

 asData - extractDataFrame(fs, addNames=TRUE)

 dim(asData)

[1] 2917013




Yet, And also, when i ran previously in oligo library, got 213067 probe 
indices 



library(oligo)


celFiles = list.celfiles(
'/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T)

raw = read.celfiles(celFiles)

exon_rma = rma(raw,target=probeset)  
#pre-processing/normalization/log2-scale

exon_mat - exprs(exon_rma)

dim(exon_mat)

head(exon_mat)



 dim(exon_mat)

[1] 213067  8


My questions,


first question is how i can get different sets from transcript and 
exon-by-exon from cell files?


and also, just curious, how is it mapped from probe sets (213K) onto 
transcript/exon level annotation(29K)?  


And, major interest is to detect differentially alternative splicings for 
each gene? (we are mostly interested in looking at those genes, e.g. 
Although a gene is differentially expressed but it is not differentially 
expressed in AS or vice versa,) how can i extract these information from 
FIRMA scores? 



could you pls let me know ?


Thanks a lot in advance, 


Sunghee




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[aroma.affymetrix] Re: transcript and exon level analysis for detection of alternative splicings

2014-09-21 Thread jjspring OH 



And one more question:

On the FIRMA scores, what are NA values, though expression levels are not 
zero?


Thanks, 


Sunghee



2014년 9월 22일 월요일 오전 10시 50분 25초 UTC+9, jjspring OH 님의 말:



 Hi,


 I would like to compare the results from plmTr and plmEx, estimation of 
 overall expression for transcripts and exon-by-exon estimation,
 but when i tried to run ExonRmaPlm with mergeGroups = T and F, 
 respectively, i am getting the identical results for following objects 
 including FIRMA scores based on 29170 rows by samples,
  


 plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)

 print(plmTr)



 plmEx - ExonRmaPlm(csN, mergeGroups=FALSE)

 print(plmEx)

 ...



 firma - FirmaModel(plmEx)

 fit(firma, verbose=verbose)

 fs - getFirmaScores(firma)

 asData - extractDataFrame(fs, addNames=TRUE)


  fs - getFirmaScores(firma)

  asData - extractDataFrame(fs, addNames=TRUE)

  dim(asData)

 [1] 2917013




 Yet, And also, when i ran previously in oligo library, got 213067 probe 
 indices 



 library(oligo)


 celFiles = list.celfiles(
 '/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T)

 raw = read.celfiles(celFiles)

 exon_rma = rma(raw,target=probeset)  
 #pre-processing/normalization/log2-scale

 exon_mat - exprs(exon_rma)

 dim(exon_mat)

 head(exon_mat)



  dim(exon_mat)

 [1] 213067  8


 My questions,


 first question is how i can get different sets from transcript and 
 exon-by-exon from cell files?


 and also, just curious, how is it mapped from probe sets (213K) onto 
 transcript/exon level annotation(29K)?  


 And, major interest is to detect differentially alternative splicings for 
 each gene? (we are mostly interested in looking at those genes, e.g. 
 Although a gene is differentially expressed but it is not differentially 
 expressed in AS or vice versa,) how can i extract these information from 
 FIRMA scores? 



 could you pls let me know ?


 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.


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aroma.affymetrix group with website http://www.aroma-project.org/.
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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 reports\tissues/RBC,QN,RMA

[aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-16 Thread jjspring OH 


Hi,

After setting up the directory, performed background correction and rank 
based quantile normalization,



library(aroma.affymetrix)

verbose - Arguments$getVerbose(-8, timestamp=T)

chipType - RaGene-1_0-st-v1

cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)

cs - AffymetrixCelSet$byName(tissues,cdf=cdf)


print(cs)


 cs
AffymetrixCelSet:
Name: tissues
Tags: 
Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
Platform: Affymetrix
Chip type: RaGene-1_0-st-v1,r3
Number of arrays: 8
Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 
7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
Total file size: 84.50MB
RAM: 0.01MB


bc - RmaBackgroundCorrection(cs)

csBC - process(bc,verbose=verbose)



qn - QuantileNormalization(csBC, typesToUpdate = pm)

print(qn)

csN  - process(qn, verbose = verbose)

plm - RmaPlm(csN)

print(plm)



Until here, looks fine, BUT, when i perform fit function as below and the 
errors come out related with directory, 

fit(plm, verbose = verbose)

qam - QualityAssessmentModel(plm)

#plotNuse(qam)

plotRle(qam)


current directory is /arom-anal, and setting up the data files (annotation, 
cel files, and raw data) look fine(see below hierarchical structure of 
directories), 
After you take a closer look at the following errors, could you please let 
me know what the problems are? 



Creating CEL file...done
[2014-09-17 13:29:59] Exception: Pathname not found: 
arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL 
(none of the parent directories 
[arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current 
directory is '/arom-anal')

  at #22. getReadablePathname.Arguments(static, ...)
  - getReadablePathname.Arguments() is in environment 'R.utils'

  at #21. getReadablePathname(static, ...)
  - getReadablePathname() is in environment 'R.utils'
  - originating from 'text'

  at #20. Arguments$getReadablePathname(filename, path = path, absolutePath 
= TRUE, 
  mustExist = mustExist)
  - Arguments$getReadablePathname() is local of the calling function

  at #19. GenericDataFile(...)
  - GenericDataFile() is in environment 'R.filesets'

  at #18. extend(GenericDataFile(...), c(AromaMicroarrayDataFile, 
uses(FileCacheKeyInterface)))
  - extend() is in environment 'R.oo'

  at #17. AromaMicroarrayDataFile(...)
  - AromaMicroarrayDataFile() is in environment 'aroma.core'

  at #16. extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, 
uses(AromaPlatformInterface)))
  - extend() is in environment 'R.oo'

  at #15. AffymetrixFile(...)
  - AffymetrixFile() is in environment 'aroma.affymetrix'

  at #14. extend(AffymetrixFile(...), AffymetrixCelFile, `cached:.header` 
= NULL, 
  `cached:.lastPlotData` = NULL, .cdf = NULL)
  - extend() is in environment 'R.oo'

  at #13. AffymetrixCelFile(...)
  - AffymetrixCelFile() is in environment 'aroma.affymetrix'

  at #12. extend(AffymetrixCelFile(...), c(ParameterCelFile, 
uses(ParametersInterface)), 
  `cached:.readUnitsCache` = NULL, encodeFunction = 
encodeFunction, 
  decodeFunction = decodeFunction)
  - extend() is in environment 'R.oo'

  at #11. ParameterCelFile(...)
  - ParameterCelFile() is in environment 'aroma.affymetrix'

  at #10. extend(ParameterCelFile(...), ProbeAffinityFile, 
`cached:.firstCells` = NULL, 
  probeModel = probeModel)
  - extend() is in environment 'R.oo'

  at #09. this(...)
  - this() is in environment 'aroma.affymetrix'

  at #08. newInstance.Class(.class, getPathname(paf), cdf = getCdf(ds), 
  probeModel = this$probeModel)
  - newInstance.Class() is in environment 'R.oo'

  at #07. newInstance(.class, getPathname(paf), cdf = getCdf(ds), 
probeModel = this$probeModel)
  - newInstance() is in environment 'R.oo'

  at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose = 
less(verbose))
  - getProbeAffinityFile.ProbeLevelModel() is in environment 
'aroma.affymetrix'

  at #05. NextMethod(getProbeAffinityFile)
  - NextMethod() is in environment 'base'

  at #04. getProbeAffinityFile.RmaPlm(this, verbose = less(verbose))
  - getProbeAffinityFile.RmaPlm() is in environment 
'aroma.affymetrix'

  at #03. getProbeAffinityFile(this, verbose = less(verbose))
  - getProbeAffinityFile() is in environment 'aroma.affymetrix'

  at #02. fit.ProbeLevelModel(plm, verbose = verbose)
  - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'

  at #01. fit(plm, verbose = verbose)
  - fit() is in environment 'aroma.core'

Error: Pathname not found: 
arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL 
(none of the parent directories 
[arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current 
directory is

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-16 Thread jjspring OH 



Hi Henrik,

See the outputs:

 path - getPath(plm) 
 print(path) 
[1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
 dir(plmData) 
[1] tissues,RBC,QN,RMAtissues,RBC,QN,RMA,merged
 isDirectory(plmData) 
[1] TRUE
 Arguments$getReadablePath(plmData) 
[1] plmData












2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:

 Ok, and then the output of: 

 path - getPath(plm) 
 print(path) 
 dir(plmData) 
 isDirectory(plmData) 
 Arguments$getReadablePath(plmData) 

 /H 


 On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshsh...@gmail.com 
 javascript: wrote: 
  Hi Henrik, 
  
  See below: 
  
  
  print(plm) 
  RmaPlm: 
  Data set: tissues 
  Chip type: RaGene-1_0-st-v1,r3 
  Input tags: RBC,QN 
  Output tags: RBC,QN,RMA 
  Parameters: {probeModel: chr pm, shift: num 0, flavor: chr affyPLM, 
  treatNAsAs: chr weights} 
  Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 
  RAM: 0.00MB 
  print(getwd()) 
  [1] /arom-anal 
  
  
  Thanks 
  Sunghee 
  
  
  2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: 
  
  That is really odd and I've never seen that error (8-9 years now). 
  There must be a simple answer to this.  What does: 
  
  print(plm) 
  print(getwd()) 
  
  output when you get to that step. 
  
  /Henrik 
  
  
  On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com 
 wrote: 
   
   
   Hi, 
   
   After setting up the directory, performed background correction and 
 rank 
   based quantile normalization, 
   
   
   
   library(aroma.affymetrix) 
   
   verbose - Arguments$getVerbose(-8, timestamp=T) 
   
   chipType - RaGene-1_0-st-v1 
   
   cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3) 
   
   cs - AffymetrixCelSet$byName(tissues,cdf=cdf) 
   
   
   print(cs) 
   
   
   cs 
   AffymetrixCelSet: 
   Name: tissues 
   Tags: 
   Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 
   Platform: Affymetrix 
   Chip type: RaGene-1_0-st-v1,r3 
   Number of arrays: 8 
   Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 
   7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] 
   Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 
   Total file size: 84.50MB 
   RAM: 0.01MB 
   
   
   bc - RmaBackgroundCorrection(cs) 
   
   csBC - process(bc,verbose=verbose) 
   
   
   
   qn - QuantileNormalization(csBC, typesToUpdate = pm) 
   
   print(qn) 
   
   csN  - process(qn, verbose = verbose) 
   
   plm - RmaPlm(csN) 
   
   print(plm) 
   
   
   
   Until here, looks fine, BUT, when i perform fit function as below and 
   the 
   errors come out related with directory, 
   
   fit(plm, verbose = verbose) 
   
   qam - QualityAssessmentModel(plm) 
   
   #plotNuse(qam) 
   
   plotRle(qam) 
   
   
   
   current directory is /arom-anal, and setting up the data files 
   (annotation, 
   cel files, and raw data) look fine(see below hierarchical structure 
 of 
   directories), 
   After you take a closer look at the following errors, could you 
 please 
   let 
   me know what the problems are? 
   
   
   
   Creating CEL file...done 
   [2014-09-17 13:29:59] Exception: Pathname not found: 
   
   
 arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL 
   (none of the parent directories 
   [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; 
 current 
   directory is '/arom-anal') 
   
 at #22. getReadablePathname.Arguments(static, ...) 
 - getReadablePathname.Arguments() is in environment 
 'R.utils' 
   
 at #21. getReadablePathname(static, ...) 
 - getReadablePathname() is in environment 'R.utils' 
 - originating from 'text' 
   
 at #20. Arguments$getReadablePathname(filename, path = path, 
   absolutePath 
   = TRUE, 
 mustExist = mustExist) 
 - Arguments$getReadablePathname() is local of the calling 
   function 
   
 at #19. GenericDataFile(...) 
 - GenericDataFile() is in environment 'R.filesets' 
   
 at #18. extend(GenericDataFile(...), c(AromaMicroarrayDataFile, 
   uses(FileCacheKeyInterface))) 
 - extend() is in environment 'R.oo' 
   
 at #17. AromaMicroarrayDataFile(...) 
 - AromaMicroarrayDataFile() is in environment 'aroma.core' 
   
 at #16. extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, 
   uses(AromaPlatformInterface))) 
 - extend() is in environment 'R.oo' 
   
 at #15. AffymetrixFile(...) 
 - AffymetrixFile() is in environment 'aroma.affymetrix' 
   
 at #14. extend(AffymetrixFile(...), AffymetrixCelFile, 
   `cached:.header` 
   = NULL, 
 `cached:.lastPlotData` = NULL, .cdf = NULL) 
 - extend() is in environment 'R.oo' 
   
 at #13. AffymetrixCelFile(...) 
 - AffymetrixCelFile() is in environment 'aroma.affymetrix' 
   
 at #12. extend(AffymetrixCelFile(...), c(ParameterCelFile, 
   uses(ParametersInterface)), 
 `cached:.readUnitsCache

[aroma.affymetrix] Errors on setup working directory

2014-09-14 Thread jjspring OH 
Hi

I am working on aroma.affymetrix package,
btw, it seems like i set up the annotationDat and rawData directory under 
the current working directory(/arom-anal) right,
but not working when i upload cdf file with cdf - 
AffymetrixCdfFile$byChipType(chipType, tags=r3)

Please see my sessionInfo() in R and also, directory information as below:

Plus, in order to easily describe the case, i have attached working 
directory image files in which annotation and cel files exist as well, 

Please let me know if there is something wrong, 


=  




In R, 



 verbose - Arguments$getVerbose(-8, timestamp=T)

 chipType - RaGene-1_0-st-v1

 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)

[2014-09-15 14:03:25] Exception: Failed to create AffymetrixCdfFile object. 
Could not locate an annotation data file for chip type 'RaGene-1_0-st-v1' 
with tags 'r3' and with filename extension 'cdf'.


  at #03. byChipType.UnitAnnotationDataFile(static, ...)

  - byChipType.UnitAnnotationDataFile() is in environment 
'aroma.core'


  at #02. byChipType(static, ...)

  - byChipType() is in environment 'aroma.core'

  - originating from 'text'


  at #01. AffymetrixCdfFile$byChipType(chipType, tags = r3)

  - AffymetrixCdfFile$byChipType() is local of the calling function


Error: Failed to create AffymetrixCdfFile object. Could not locate an 
annotation data file for chip type 'RaGene-1_0-st-v1' with tags 'r3' and 
with filename extension 'cdf'.

 








 help(AffymetrixCdfFile)

 getwd()

[1] /arom-anal

 quit()

Save workspace image? [y/n/c]: n

verdas-MacBook-Pro:arom-anal sungheeoh$ ls

annotationData rawData

verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/

verdas-MacBook-Pro:annotationData sungheeoh$ cd ..

verdas-MacBook-Pro:arom-anal sungheeoh$ cd rawData/

verdas-MacBook-Pro:rawData sungheeoh$ ls

tissues

verdas-MacBook-Pro:rawData sungheeoh$ cd tissues

verdas-MacBook-Pro:tissues sungheeoh$ ls

RaGene-1_0-st-v1

verdas-MacBook-Pro:tissues sungheeoh$ cd RaGene-1_0-st-v1/

verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls

CS _ 10_(RaGene-1_0-st-v1).CEL CS _ 7_(RaGene-1_0-st-v1).CEL NS _ 
1_(RaGene-1_0-st-v1).CEL NS _ 4_(RaGene-1_0-st-v1).CEL

CS _ 12_(RaGene-1_0-st-v1).CEL CS _ 8_(RaGene-1_0-st-v1).CEL NS _ 
3_(RaGene-1_0-st-v1).CEL NS _ 5_(RaGene-1_0-st-v1).CEL

verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ cd ..

verdas-MacBook-Pro:tissues sungheeoh$ cd ..

verdas-MacBook-Pro:rawData sungheeoh$ cd ..

verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/

verdas-MacBook-Pro:annotationData sungheeoh$ ls

chipTypes

verdas-MacBook-Pro:annotationData sungheeoh$ cd chipTypes/

verdas-MacBook-Pro:chipTypes sungheeoh$ ls

RaGene-1_0-st-v1

verdas-MacBook-Pro:chipTypes sungheeoh$ cd RaGene-1_0-st-v1/

verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls

RaGene-1_0-st-v1.r3.cdf

verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ R




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   



Thanks, Sunghee


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